Mystery of the Phantom
by Marcus S. Lazarus
Summary: -AU, Part 2 of series- As their second year in Atlantis begins, Elizabeth finds herself drawn ever further into the mystery of the Phantom of Atlantis, while John finds himself constantly torn between what he has become and what he wishes to be...
1. It's a New Dawn

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This marks the second part of my "Phantom of Atlantis" series, an AU take on "Stargate Atlantis" where John Sheppard, instead of being the city's military commander, is a mysterious masked figure who has been living in Atlantis and fighting the Wraith for almost two decades prior to the expedition's arrival in the city; reading the first story- "The Phantom of Atlantis"- will be required to understand what's going on here in greater detail

AN 2: Thanks are due to Manic Penguin, whose story 'Connections' inspired some of the plot elements in the upcoming few chapters (All of which are naturally used with her permission)

Mystery of the Phantom

Sitting in the SGC conference room opposite the newly-appointed General Hank Landry- General O'Neill had apparently left for his new Washington assignment shortly after their return from Atlantis; he claimed that he'd only stayed around as long as he had to make sure everyone got back all right-, Elizabeth was already beginning to feel anxious about this meeting.

The traditional check-ups in the infirmary had proceeded fairly smoothly, which was something that Elizabeth was definitely grateful for. McKay had complained about the needles, of course, but that was just something she'd come to expect by this point; the only _truly _frustrating detail had been the sheer length of time they'd spent there as everyone's medical records were updated to compensate for their year away, and that was only because going over your health for the past year had never been something Elizabeth had particularly enjoyed doing.

The subsequent debriefings as she and the rest of her staff went over some of the details in the respective mission reports of their various department members proved to be rather difficult at times, of course. Kavanagh alone seemed to be complaining that he had been unjustly forced out of his position despite the fact that it was hardly anyone else's fault if nobody liked him, while Peterson seemed to alternate between being grateful to be away from Atlantis and being angry at the fact that everyone seemed so unsympathetic towards the fact that he'd nearly died when those nanites had infected him…

Even with all those issues put aside for the moment, however, now that she was actually being called upon to justify their latest request for new staff and resources, Elizabeth couldn't help but feel grossly out of practise at this particular type of meeting. As much as she might like to regard herself as an accomplished diplomat, the fact remained that she hadn't actually been engaged in any actual large-scale diplomatic relations since she found herself in Atlantis; what negotiations she _had _carried out had been relatively 'small-fry' compared to what she was dealing with at present.

Negotiating some temporary treaties and alliances with people in the Pegasus Galaxy to gain food in exchange for their promises of future protection wasn't the same as talking to the SGC on Earth, no matter how much she might want to act like it was. For one thing, if she didn't manage to make her case in Pegasus the worst that could happen was the people of her city had to go without food for a short while; if she failed to make her case here, she stood a very good chance of access to Atlantis being cut off for good, or at least losing some of her staff if her superiors decided that they'd prefer to cut back on the military or scientific divisions of the city (The presence of the Wraith might prompt some people to either cut back on sending out teams to other worlds, thus lessening the need for a military division, or the need to deal with the Wraith might prompt them to withdraw some of the scientists; Elizabeth couldn't know which would turn out to be the case).

"Right then," Landry said as he looked at her, his tone an interesting combination of seriousness and a light trace of humour, "first things first, while there's an expected level of cannibalism from the SGC, take into account that we do still have issues to deal with in _this _galaxy even with the Goa'uld having been virtually eliminated, so have your people keep that in mind when attempting to poach my people."

"I'll remember that," Elizabeth replied, allowing herself a slight smile at the general's response. The earlier debriefings on mission reports had been conducted in front of a larger group of SGC officials to make sure everything was covered from all relevant angles, but with the current meeting it had been decided that a more individual approach with both leaders bringing their staffs' concerns and requests forward would work best. "Of course, the advantages of access to a fully-powered ZPM make it easier for us to recruit further staff, given that Atlantis is no longer such an uncertain long-term project."

"Yes, Homeworld Security has already noted the obvious benefits in your requests to get additional resources supplied now that you've established what we might need for further reconnaissance efforts in Atlantis," Landry said, nodding slightly at her before his expression became somewhat grimmer. "On that topic, Colonel Carter asked me to confirm that you are aware that not all the scientists on your list can be made available to you; the red flags that would go up as a result of that many major names disappearing would attract too much attention for anyone to conceal."

Having already anticipated a comment like that- she might have been out of touch with current events on Earth but she doubted things had changed _that _much-, Elizabeth responded with the more cautious reply.

"Given that we now have the ability to regularly maintain contact with Earth, both through the Stargate and the _Daedalus_'s ferry runs, the general cover story of a scientific expedition of a classified nature should prove sufficient in most cases," she said, looking back at the general with a casual gaze. "Coupled with the fact that we're actually able to provide an effective time frame of how long we're expecting the staff to commit to the project, I don't foresee any serious problems with getting further staff. Besides, at present Atlantis is barely operating on more than a skeleton staff at this time, and I think we can all agree that an endeavour of this magnitude requires more than that."

"Quite," Landry said, nodding briefly at Elizabeth before he looked at her with a far grimmer expression. "On a related topic, more than one member of those government agencies aware of the SGC has expressed… concern… about the continued presence of the individual known as 'the Phantom' within Atlantis."

"The Phantom?" Elizabeth repeated, trying to sound casual even as she was inwardly crossing her fingers; she _had _to remember to watch what she said about this particular issue…

"While nobody can deny that his actions did indeed prove helpful towards us during the siege of Atlantis, as well as providing you with other assistance while you were isolated from Earth," Landry continued, his expression becoming increasingly solemn as he stared at her, "we also have to keep in mind the possibility that his agenda might change at some future date; just because he's worked to our benefit so far doesn't meant that he'll continue to do so."

For a brief moment, Elizabeth wished that she could mention what she knew about the Phantom to try and act in his defence, but quickly stopped that thought before it could go any further; the last thing she wanted was to give away how she knew the Phantom wouldn't do anything against them (Especially when even she had to admit that her 'knowledge' was based more on feelings than anything else).

"As my reports have indicated," she said, trying to bring the conversation away from a potentially dangerous area, "Colonel Sumner and I are working to do what we can to apprehend the Phantom, but so far he has proven exceptionally skilled at evading capture; even when he returned one of our gateships after using it to detonate a naquadah generator, he somehow managed to evade our teams without anyone even seeing him depart from the gateship in the first place despite an entire team being dispatched to apprehend him as he returned."

"Yes, I read that in the files," Landry continued, his expression becoming increasingly grim as he looked at her. "Actually, the issue with those nanites is actually a particular example of one of the main points of concern at this time; some of my superiors are naturally… uncomfortable… about the obvious implication that he was aware of their existence and chose not to warn anyone about them."

"If you'll consult the reports, you'll note that Doctor McKay stated that the nanites were released due to flooding damage sustained in the storm," Elizabeth responded, folding her arms as she looked at Landry. "Admittedly, it would have been helpful if we had been made aware of their presence regardless, but given that, if it hadn't been for the storm, we would have simply discovered the nanites while they were still contained, and hence no danger to anyone who knew enough about what they were doing."

"True," Landry said, nodding slightly in recognition of Elizabeth's point. "However, there are other factors to consider, most notably the issue of that shield he programmed to activate whenever you dialled this galaxy."

"Again, the files clearly explain that that program was installed before any of us even arrived in Atlantis; the obvious assumption would be that the Phantom set that up to prevent the Wraith from gaining access to this galaxy after learning where they went after leaving Pegasus after he consulted the city's databanks," Elizabeth replied, already cursing herself for her last statement as soon as she finished saying it; speculation like that wasn't the best way to avoid attracting attention to her opinion on the Phantom.

"I don't deny that it would have been far more beneficial for us if he had deactivated that program as soon as he could," she continued, knowing even as she spoke that she was walking a fine line between being objective and giving away more than she might like about her… interest… in the Phantom, but nevertheless resolved to continue, "but when you consider that we are technically the intruders in this situation- he _has _lived in Atlantis, according to all reports, for almost two decades before we arrived there-, the fact that he has taken no action to drive us out of the city since our arrival- indeed, he has taken action more than once to allow us to remain in this city when he could have easily driven us out- is something that we shouldn't overlook just because he operates independently from our own command structure."

"Nobody is denying that the Phantom's presence has proven vital to your expedition's survival at crucial moments, Doctor Weir; what they object to is his continued status as an independent element rather than operating within a defined command structure," Landry replied; for a moment he seemed to be looking at her in an apologetic manner, but then the moment passed and he was simply staring grimly at her once again. "Your point about him having lived in Atlantis for longer than us is a valid point, don't get me wrong, but many people feel that, if he's willing to have us live there in the first place, he should be equally willing to allow us greater access to whatever knowledge or information he has to share. The fact that he has so far told your team _nothing _about his knowledge of Atlantis beyond what you needed to know at a time of crisis has several people understandably concerned that he has some hidden agenda that we are as yet unaware of."

"You can assure your superiors that we are making all possible effort to apprehend and question the Phantom about his knowledge of Atlantis; as we have already mentioned in our reports, that knowledge of the city that makes him such a valuable target also makes him rather difficult to have a conversation with in the first place," Elizabeth replied, trying not to think about those moments when he'd visited her on the balcony; in the end, it couldn't exactly count as questioning him when _he _was always the one who made the decision to initiate contact in the first place. "Should they need further details about our plans regarding the Phantom, Colonel Sumner is the person to ask for information; he has final call in military-related matters, after all."

"Naturally," Landry said, nodding briefly back at her, a slight smile visible at the corner of his mouth- Elizabeth chose to take that as a good sign; hopefully she'd given him something to think about-, before the smile faded and his expression became more solemn once again. "Getting back to the matter of staff…"

Even as she responded to Landry's words, however, Elizabeth couldn't shake the concerns that his earlier comments had sparked off in her mind.

What would happen to the Phantom now?

Sumner might have allowed him to escape once, but would that decision reflect a new policy towards the Phantom's existence overall, or was it strictly a one-time method of 'repaying his debt' (Or something like that; Elizabeth would be the first to admit that she wasn't up on the fine details of military terms even if she had spent a significant portion of her life working to achieve negotiations to prevent military action being required by anyone) to the Phantom for helping to protect Atlantis?

Elizabeth didn't know.

More to the point, she didn't know why it _mattered _to her so much; how could this man have captured her interest like this when she didn't even know his _name_…?


	2. It's a New Bond

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Mystery of the Phantom

"All right," Elizabeth said as she sat around a table in the commissary, looking at Sumner, McKay and Beckett as they ate their various lunches; no matter how good some of the food in the Pegasus Galaxy had been, there was no real substitute for the foods they'd grown up with over the years. "Now, everyone's clear on the current timetable?"

"Seems straightforward enough, anyway," McKay confirmed, tucking into a plate of something Elizabeth couldn't immediately identify save for the fact that it definitely wasn't lemon chicken (McKay had practically emptied out the commissary of everything _but _the aforementioned food upon his arrival). "I spend a few days in Area 51, Sumner and Carson go over personnel files and any new equipment they've picked up here while we're away, and you're off to Washington to get everything straightened out regarding how many people we can request for the upcoming year?"

"Essentially, yes," Elizabeth confirmed, nodding briefly back at McKay and wondering how much longer she could allow him to get away with repeating himself before she could legitimately tell him to stop it; she was fairly sure she'd gone over the timetable at _least _a dozen times by this point. "We've only got around a couple of weeks before the _Daedalus _gets back to Earth and gets checked over for the return trip; given that it should take the better part of the first week for me to sort out specific numbers for you all, that time is generally free to do what you will with it."

"Well, that's good to know at any rate; been meaning to visit my family since I got back here," Carson said, smiling briefly at the thought even as he continued to chew his sandwich. "A few days back should be enough for her, anyway…"

"Quite," Sumner said, nodding briefly at Carson before he looked back at Elizabeth with an expression that she couldn't quite identity. "I'd… well, I've got a few people I need to see myself."

"Colonel Everett's family?" Carson asked, looking at Atlantis's military leader with a slightly uncertain tone; the colonel had yet to discuss his feelings on Everett's sudden loss of approximately a decade's worth of life energy, but Elizabeth had been informed that Sumner had been seen in the medical bay looking at the bed where Everett had been examined before his return to Earth.

"Among others," Sumner said briefly, evidently uncomfortable with taking that conversation any further. Elizabeth briefly thought about asking him for further information, but swiftly decided against it; as McKay had pointed out more than once, Sumner wasn't the type of military commander who spent much time in social conversation with the rest of his team.

"Right…" Elizabeth said, glancing down at her watch before she sighed and stood up. "Well, I'd better be off; I still have to make sure everything I need from here is packed before my flight."

"Have a good trip," Carson called after her, prompting Elizabeth to nod in response before she walked out of the commissary, heading for her office as the rest of the Atlantis senior staff continued to eat their assorted foods.

For a moment, as she paused at the door to look back at the small group of people who'd almost become a new family to her over the past year- Sumner was admittedly more of a distant cousin than a particularly close relative, but Elizabeth had been surprised to find that she'd actually become rather fond even of Rodney McKay despite his occasional arrogance, and Carson was rather like a slightly-distant-while-still-fond-of cousin-, she allowed herself a smile at the sight of her three department heads back on Earth at last, but then shook it off and turned back to head down the corridor.

Nostalgia for life back on Atlantis and any bonds she'd formed there- even if she doubted that Sumner would regard there being any particular 'bond' between them; he might have grown comfortable in the city, but his attitude when off-duty made it clear that she and the others were only colleagues to him- could wait until she got back from Washington; right now, she had business to attend to.

* * *

A few hours later, as Elizabeth sat in the airport waiting area for their plane to be ready- why was it that her transportation always seemed to be delayed these days?-, she was almost grateful to have an opportunity to study an actual newspaper; it might not be the kind of leisure reading she preferred for a long flight, but it gave her a good chance to catch up on some of the events that had been happening on Earth since she was last present.

The only problem was that none of the stories she was reading could successfully hold her attention for any length of time now; no matter how hard she tried, her mind still kept on drifting back to concern for the man who had saved the city she already considered 'hers' without her ever having seen more than the lower left side of his face.

She just wished she knew what it was about the Phantom- it was best to think of him as 'the Phantom' right now; if she started referring to him as 'John' regularly in her head there was a chance she'd say it to someone and give away the time she'd spent with him- that constantly kept her thoughts coming back to him; he was just so… _different _from the people she normally-

The _people she more regularly found herself spending time with_, was the best term she could come up with to describe her relationship with him; certainly she'd never met anybody else who could control Ancient technology with that kind of ease, to say nothing of his evidently exceptional knowledge of the city itself…

"Something up?" General O'Neill's voice said, breaking into her train of thought.

"Pardon?" Elizabeth asked, looking up at him in confusion.

"You've been staring at that page for the last few minutes without ever turning it; either there's a _very _engrossing photograph there or you've got something on your mind," O'Neill said by way of explanation. "So, which is it?"

"Just… wondering how things are back in Atlantis," Elizabeth replied; it was, after all, _almost _the truth, even if she was thinking more about a specific individual than the city as a whole.

"Got pretty attached to the place, huh?" O'Neill asked.

"More than I expected, really," Elizabeth admitted. "I actually miss the waves more than anything else; I had trouble getting to sleep the last couple of nights because my room was too quiet."

"Yeah, it's funny what gets to you; when I was stuck on this planet Edora for a few months some years ago, it took me a while to get used to sleeping there regularly because it was too quiet and I wasn't expecting anything to try and kill me," O'Neill replied, smiling briefly at the memory before he noticed Elizabeth's inquiring expression. "Y'know, when I was doing overnight missions through the 'gate I always had to be ready in case something tried to sneak up on me during the night, but with the 'gate being buried and the Edorans being perfectly friendly I didn't even have that concern…"

"Oh," Elizabeth said, nodding slightly in understanding- she _thought _she understood where the general was coming from with his last statement, even if she didn't quite see things that way herself-, before she glanced over at the transport plane visible through the windows of the waiting area. "How long is that going to take?"

"Depends on what's up with it," O'Neill said briefly, before he looked back at her in a more pointed manner, a slight smile on his face as he spoke. "Anyway, getting on to a more… interesting topic, how does it feel to be Atlantis's answer to Commissioner Gordon?"

Elizabeth blinked.

"Uh… excuse me?" she asked, looking at the general in confusion; she couldn't exactly see where the similarities were between her and the chief of police in the _Batman _series.

"Y'know, be the person in a position of official authority who's pretty much the only guy trusted by the local masked vigilante?" O'Neill elaborated, waving a hand promptingly at he smiled at her. "C'mon, you're telling me the analogy _never _occurred to you…?"

"I'd hardly say that I could be considered someone the Phantom 'trusts'," Elizabeth replied, even as her mind raced to try and work out what had led the general to make that comparison; nobody else was aware of her secret meetings with the Phantom aside from the two of them, and they'd barely spent any time alone together during the Wraith assault to encourage the idea that there was anything between them…

"Yeah, I'm not sure I'm buying that," O'Neill replied, his smile assuming a slightly teasing aspect as he looked at her. "From what I've read about the guy, the Phantom certainly sounds pretty 'Batman'-y; after all, a guy in a mask with a lot of training but no other apparent powers- disregarding his apparent Ancient gene; when you get down to it that just makes it easy for him to use what he's got rather than giving _him _anything extra- guarding a city? Add on the fact that he specifically asked for you to be left 'in the loop' during the siege when- according to all reports- Sumner and Everett would have been perfectly willing to take complete control of the situation themselves…"

His voice trailed off as he looked at her, evidently trying to prompt her into continuing his line of reasoning, but Elizabeth simply stared back at him with an expression that Jack would later describe to his friends as being 'more neutral than Switzerland'.

"Your point about the… 'Batman' similarities makes a certain sense when you explain it like that," Elizabeth said at last, nodding slightly in concession at the general, "but I have to disagree with your description of me as the 'Commissioner Gordon' to the Phantom's 'Batman'; he simply requested my presence during the siege because he felt that I was the only member of the expedition's senior staff he could trust to work with him without attempting to take advantage of his presence to try and capture him at some point."

Privately, Elizabeth wished she could come up with a better way to phrase what she'd just said- she might not have explicitly said that she agreed with the Phantom's assessment of the situation, but she still felt as though her opinions on Atlantis's military commanders made itself fairly clear in her words-, but she couldn't change the facts; John had _specifically_ said during the siege that he trusted her.

Admittedly, Elizabeth had to confess that she would probably have taken his side in that confrontation even if his appearance in the conference room before the siege _had _been their first 'proper' meeting (Discounting the incident during the Genii invasion); her diplomatic background would have practically insisted that they cooperate fully with a man capable of offering them the kind of assistance that John had been able to provide them with…

"Still proves my point," General O'Neill said, smiling briefly at her as he spoke. "Somehow, I get the feeling you're going to be seeing a bit more of that guy as things go on in Atlantis; you might want to look into getting a 'PhantomSignal' so he knows when you need his help with something…"

"I'll keep that in mind, general," Elizabeth replied, already noting to herself that the 'signal' concept might not even be needed; she might not have a 'Bat-signal' as such, but the memories of her conversations with the Phantom on her balcony made it fairly self-evident that she did have a connection to the Phantom beyond what she was claiming to have…

"So," she said, realising that the current topic of conversation at least made it easy to address one of her own issues, "what's… _your _opinion on the Phantom?"

"My opinion?" O'Neill replied, looking at her with a suddenly serious expression. "Officially, I have to agree with the general ruling of Colonel Sumner; the Phantom is a dangerous independent operative in a situation where stability and security are paramount, and the colonel's efforts to capture him so that we can find out where he acquired his knowledge about Ancient technology remain paramount."

"And… _un_officially?" Elizabeth asked, looking at him with a slight smile.

"Unofficially?" O'Neill replied, shooting another brief smile at her. "Quite frankly, I'm just jealous that you guys managed to get yourselves your own personal superhero; do you know how many planets I visited and there wasn't even a single heroic _myth_ about somebody with superpowers?"

"Right…" Elizabeth said, smiling slightly at the general before she assumed a more serious expression. "So… if, for example, I'm a bit… lax… in arranging patrols to find his hiding place?"

"Eh, it's not like anybody's here's going to be that concerned about you not finding the guy; so long as he doesn't do anything to hurt your chances of survival out there you'll probably be fine with the whole 'live and let live' policy where he's concerned," O'Neill said reassuringly. "Of course, so long as you can give tomorrow's delegates some interesting stories about one of their countrymen having saved a dozen or so people at some point during the expedition, everything should probably go fine there too."

"Are you suggesting I exaggerate the qualities of members of my staff to win support?" Elizabeth asked, raising an eyebrow pointedly as she looked over at her replacement as SGC commander.

"Something along those lines, yeah," O'Neill said, nodding slightly reluctantly under Elizabeth's pointed stare. "Hey, I know flattery won't get you everywhere, but every little bit helps keep the wheels turning, right?"

Elizabeth had to admit, General O'Neill did make a point; if nothing else, after the Phantom's presence had caused so much upheaval in the city- she'd overheard more than a few conversations among the staff about the implications of Atlantis having its own 'superhero' in the mess hall-, anything she could do to improve her image in the eyes of the diplomats would probably be a good thing.

She just hoped that she could get through the next couple of days without too many problems; even after her meeting with the diplomats was over, she still had more than a few… personal issues… to deal with once she was finished in Washington.


	3. The One I Need, Not the One I Want

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Not entirely certain about this chapter, but I felt that it had to be written; best to get this issue out of the way _before _Elizabeth goes back to Atlantis, after all…

Mystery of the Phantom

Even Elizabeth wasn't sure how it had happened, or how she had come to the decision to do this in the first place, but the facts remained what they were; here she was, on her first real 'day off' since she'd arrived in Atlantis over a year ago- as the final authority for pretty much any major decision in the city without the ability to contact Earth, it was practically impossible for her to have a day off in the Pegasus Galaxy-…

And she was sitting in front of the house she had purchased with Simon when they'd made the decision to move in together, trying to decide how to phrase what she was about to say in what would almost certainly be her last conversation with the man she'd been prepared to spend her life just over a year ago.

She'd had a lot to deal with before she reached this point, of course; the talks with the various diplomats responsible for overseeing the Stargate Program alone had taken her several hours to get through, even if it had been far easier than what the reports said about the original meeting to introduce the Stargate to other foreign powers. The Chinese delegates were still disgruntled at the whole thing, and she couldn't shake the feeling that the Russian delegates were eventually going to ask for more than what the SGC would be willing to share with them, but in general the whole thing turned out to be very cordial.

In the end, even the death toll sustained during the siege hadn't been met with that much shock.

Actually- and ironically, in Elizabeth's opinion-, the thing that attracted the most attention was the _reason_ for the low death toll at the time; the presence of the Phantom and his control over- and knowledge of- Ancient technology.

As much as they acknowledged the merits of his assistance so far, the general consensus of the delegates agreed with Sumner's original assessment of the Phantom; as a dangerous renegade element in a situation where stability was paramount for survival, it was vital that he be apprehended so that they could determine his true agenda and learn what else he might know about the city for future defence purposes. They were resupplying the Atlantis armoury with any Earth-originated weaponry Sumner's staff had confirmed was particularly effective against the Wraith- anti-aircraft guns, taser guns, that kind of thing-, but none of the delegates, for all their other minor disagreements, seemed to differ in their belief that the Phantom's knowledge was a resource that they had to have access to as soon as possible.

Elizabeth was just grateful that she didn't have to worry about anybody trying to replace Sumner with someone who'd enforce tighter restrictions on the city in his efforts to find John; as it was, Sumner's attitude towards finding the Phantom so far had apparently only increased the delegates' willingness to recommend that the city's senior staff remain unchanged.

Admittedly, the additional military forces they were receiving at this time might make it harder for John to stay hidden in the city, but given Sumner's implied willingness to accept the Phantom's presence in their last encounter, the situation could definitely be worse…

…And Elizabeth had to stop thinking about everything that had happened in the recent conferences; there wasn't any _point _to thinking about that stuff now.

She'd done what she could at the meeting and it had all gone as well as she could have expected; the main thing was that everyone who had come through the Stargate- with the obvious exceptions of Kavanagh and Peterson, assuming anyone would even miss them after the way they'd been the last few months- were going back to Atlantis, even if John would now 'officially' find it harder to get around…

She _had _to stop this; going over a concluded meeting wasn't helping anything. All that thinking back on it served to do at this point was distract her from what she _should _be thinking about right now; specifically, the state of her relationship with Simon and the reasons for her presence here.

After spending the past year on virtually the other side of the universe from the man she'd agreed to marry before she was given the assignment at the SGC, during which she _should _have- according to all conventions regarding relationships- spent that time thinking about him, she'd barely thought about him more than maybe a dozen times of her own accord when some outside circumstances- mostly medical-related- hadn't directed her thoughts towards him.

No matter what she might have felt for him before travelling to Atlantis, it was fairly clear to her that any feelings she may have had for him in the past weren't a factor in any relationship she had with him any more.

She couldn't entirely understand how she'd reached this point herself, but she could hardly help how she felt; here she was, about to face Simon again for the first time since leaving Earth (Not counting that meeting she'd had with him in that illusionary world created by those 'cloud creatures')…

And all she could find herself thinking about was a man in a mask and a cloak who killed people with an ease that should have terrified her, hadn't shown her what he looked like underneath the mask, and hadn't even told her his last name (A part of her reflected that he may not have even given her his _first _name, but she pushed that aside; whatever else she might be, she knew when people were lying to her, and she remained certain that John _had _been telling the truth about his first name)?

It didn't make sense…

_No_, Elizabeth told herself, stopping that train of thought before it could develop further. _It _does _make sense… you just don't want to admit _how _it makes sense_.

The ease with which she'd started wanting to learn more about the Phantom was a point of concern, she knew- John certainly wasn't the type of person she'd have _ever _pictured herself… thinking about… in this kind of context-, but in the end it was just the final catalyst rather than anything else; what she was about to do had had the potential to happen long before she even heard of the Stargate…

If she was perfectly honest with herself, no matter how much she might have worked to think otherwise, she had never been _completely _certain about the relationship with Simon from the beginning.

If she'd been as committed to him as she'd believed she was in the past, surely she never would have left for Atlantis in the first place; her later realisation about the lack of interest he'd shown in her work had only served as a further catalyst for the train of thought that had led her to this position.

Her subsequent… thoughts… about the Phantom since encountering him in Atlantis might have left her interested in learning more about him, but even trying to pass them off as nothing more than curiosity about a man whom she possessed so little background information about didn't change the fact that she'd spent more time in the past year trying to spend time with the Phantom than she'd _ever _spent looking for opportunities to be with Simon in the year before leaving Earth.

She'd _spent _more time with Simon than she'd spent with the Phantom over that time frame, she wasn't denying that, but when she looked back at her time with Simon, the vast majority of their meetings had been little more than the usual encounters you'd expect to have with someone who shared the same residence as you. They'd shared more than the occasional meal together, and there'd been the… nights… as well, but somehow… she'd never felt the same kind of _spark _she felt whenever she was spending time with the Phantom; the feeling that she was simultaneously treasuring everything about his presence and wishing she had more to say to him.

When it came to Simon, in the end, his main appeal for her back before she'd left for Atlantis had been the fact that he was… safe, she supposed was the best term for it; she had always known he'd be there for her, and thus didn't have to worry about the risk of him hurting her, either deliberately or unintentionally.

As reassuring as that aspect of his personality had been… it wasn't what she was looking for any more.

Elizabeth wasn't sure how it happened, but, at some point during her time in Atlantis, she'd reached a point where she didn't recognise who she'd been when she'd left; all that she knew for certain now was that, while she still appreciated certainty in her life, the type of stability that a life with Simon had offered no longer appealed to her any more.

Whether it was just spending a year facing the threat of an alien race who consumed your very life energy, spending a year in the constant presence of the military, or simply spending a year knowing that she had a city with its own personal superhero- it might be a childish term, but how else was she to think of a man in a mask who helped keep Atlantis safe?-, she felt that she'd become less…

_Naïve_, was the best term she could use; looking back, the woman she'd been before hadn't _really _understood what she was getting into back then.

It wasn't that she'd stopped believing in diplomacy, but her confrontation with the Genii in particular had taught her that sometimes you couldn't depend on diplomacy to get you out of a situation; sometimes, you had to rely on a more physical approach to get the job done…

In the end, the fine details about _why _she wasn't who she had been didn't matter; all that mattered, in the end, were the reasons she was here

Taking a deep breath, Elizabeth stepped out of the car and walked towards the house, taking a deep breath before she knocked on the door, taking a deep breath as she waited for a moment before Simon finally opened the door.

As she looked at him, staring uncertainly at her- her earlier phone call to let him know she was back hadn't been particularly straightforward, but she'd at least been able to deal with the obvious questions of when she'd come back-, she could only smile back at him.

"Hello, Simon," she said at last, already kicking herself for the statement; how was it that she could negotiate treaties between warring nations on her coffee break but couldn't seem to straighten out her personal life to any real degree? "I know this is… short notice, but…"

"Elizabeth?" Simon asked after she'd stood on the door in silence for a moment, evidently confused by her actions. "Is… something wrong? I… I mean, I got your message, but you didn't…"

Registering the evident discomfort on her face, Simon trailed off himself, the two of them simply standing and staring at each other as each of them tried to decide what to say next.

"Look, this is… can I come in?" Elizabeth asked at last, looking at Simon with a regretful, uncertain smile that she had a feeling told him what she was there to say more than any words could.

The fact that Simon almost automatically fell silent and nodded as he stepped back to allow her in confirmed Elizabeth's earlier theory, but simultaneously strengthened her resolve to continue.

She was in the house; now it was up to her to say the words that would end her life here for good.

"Simon…" she said, pausing for a moment to collect her thoughts one last time as she looked at him, trying not to think about a man with a thinner build who somehow managed to look stronger than Simon ever had, who had been there for her at a time in her life like nothing she could have ever imagined. "Before I go any further, I have to tell you that I'll always… _care _for you, and I have enjoyed our time together…"

"But…?" Simon said after another moment's silence (God, Elizabeth hadn't been this uncomfortable when she was alone with the _Phantom_, and that man had shot peoples' _limbs _off).

"But… this…" Elizabeth continued, waving a hand in a vague manner that even she wasn't sure about the purpose of- was she 'indicating' the house, or was it a general reference to Earth itself?-, "it isn't who I am any more. I've… I've _changed_, Simon; who I was here… with you… I'm not sure I _recognise _that person any more…

She paused for a moment, wishing there was a better way to say this, but knowing that Simon had to hear it. "And… I'm not sure that who I am can be with you the way I was back then."

"Is this… anything to do with the fact that I haven't signed up?" Simon asked, looking at her with a slight uncertainty (Elizabeth _did _recall asking the SGC to see about recruiting Simon for the Atlantis medical staff, but she hadn't been sure if they'd go for it; in the end, it had almost been done more out of habit than anything else). "It's just that… well, I'm still making up my mind; I have patients here, responsibilities…"

"It's not that," Elizabeth responded, shaking her head briefly to cut him off. "I understand that you have responsibilities here, and I'd never ask you to leave them if you thought you could do more good here than there, but in the end…"

She swallowed slightly, unable to believe what she suddenly found herself about to say. "There's someone else."

As soon as the words were out of her mouth, she couldn't believe she'd uttered them.

_Someone else_…

A 'someone else' who went around in a mask and a cloak, practically never spoke to her unless there was some upcoming crisis or urgent piece of information he needed to pass on to her, had only given her a name that could just as easily be fake as it could be real, killed with an ease that she consciously knew should have terrified her…

And yet, at the same time, John, or the Phantom, or whatever he wanted to call himself, represented a mystery that she wanted to solve, a question that she wanted to answer… and a man who lived his life with such an intensity and passion for everything in it that a part of her, she only now realised, couldn't help but wonder how it would feel directed at _her_.

Even if she knew so little about him, when she was close to him…

When he looked at her…

What she felt during those moments was so confusing, so uncertain, so… _indefinable_… that she already knew she'd be no good in a relationship with another man until she'd had the chance to sort out her feelings for the most mysterious man she'd ever met.

"Oh," Simon said, his expression unreadable as he looked back at her. "I see."

"I didn't _plan _it, and nothing's… _happened _yet," Elizabeth said, suddenly needing to assure him that, whatever else had happened, she hadn't been unfaithful to him. "But… even if he _wasn't _there…"

She swallowed, her throat suddenly as dry as if an entire desert had been dumped down it, before she slightly shook her head to push those thoughts aside and looked resolutely at Simon. "This… isn't who I am any more, Simon. I'm sorry."

"I see."

That was all Simon said to her, but the sorrow he was feeling was obvious.

"You… you shouldn't be," Elizabeth said at last, trying to sound reassuring even as she knew how hollow what she was saying would sound in this situation. "Trust me; who I am now isn't who you fell in love with. It might be… harsh… now, but it's for the best in the long run."

"I… see…" Simon said again, nodding slightly at her before he stepped back, indicating the house. "Do you… need anything?"

Elizabeth could only shake her head at that; most of her more personal possessions had been moved into storage in the SGC before she went to Atlantis, and what was left at Simon's wasn't anything that couldn't be easily replaced later on.

"Goodbye," she said one last time, before she turned around and walked out of the house, leaving that part of her life behind herself for good.

At least with the Simon situation dealt with she could get back to the problem of sorting out some of her new staff requests; Doctor Jackson alone would make a valuable addition to the team, but the problem lay in being able to convince General O'Neill to allow him to leave the SGC in the first place…

Those were the issues she had to focus on now.

Those were the issues she was _meant _to focus on.

If only concern for the man in the mask she'd left back in her city didn't constantly sneak into her thoughts whenever she thought about the alien world that had become her home…

* * *

AN 2: So, just to check, is there anything else on Earth anyone wants to see, or shall I just get on to the new take on "Intruder" next chapter and leave Earth in the past?


	4. Slowly Getting Closer

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Thanks to everyone who offered their opinions on this chapter; having weighed all possible options, I decided to get straight down to the events of "Intruder" while looking at Sumner's attitude towards recent events in Atlantis; I figured I could cover his thoughts on the Phantom in transit as easily as I could look at them while he was on Earth

Mystery of the Phantom

As Elizabeth sat in the dining area on board the _Daedalus_, sipping on a cup of coffee- one definite advantage of renewed contact with Earth; a superior quality of coffee to what she'd been drinking since arriving in Atlantis- she allowed herself a slightly wistful smile as she stared out at the sight of the blurring blue of hyperspace passing by outside the window, taking her closer and closer to Atlantis with each passing moment.

According to the latest report from McKay, the ship had recently re-entered the Pegasus Galaxy and was now only a couple of days' travel away from Atlantis; after almost two weeks of being cooped up in the ship to take a trip that had only taken a matter of moments to complete the first times she'd travelled through the Stargate, Elizabeth was looking forward to being back in her city.

And _no_, she told that small, traitorous part of herself that never seemed to shut up, her eagerness to be back in Atlantis had _nothing _to do with a certain masked individual…

She just couldn't understand it; admitting to Simon that there was someone else was one thing, but actually _doing _something about that 'someone else' when she had so little idea about who he was…

Elizabeth would be lying if the thought didn't make her feel… _uncomfortable_; there were so many unanswered questions when it came to Atlantis's mysterious protector that she didn't even know where to _begin _to find the answers…

It wasn't that she doubted John's loyalty to Atlantis- the fact that he'd simply stayed hidden when his apparent knowledge of the city would have allowed him to eliminate most of the people who opposed his presence with relative ease alone said a great deal about what kind of person he was-, but how could she feel… what she felt… about him when she knew virtually nothing about his past? Even now, She didn't know where he came from, she didn't know how he'd arrived in Atlantis, she didn't know _why _he spoke to her rather than anyone else…

And yet… somehow, when she was with him… or even when she just casually thought about him without considering such issues as Sumner's problem with his presence… none of that mattered.

All that mattered- all that she _cared _about in those moments- was being with John; whether it was talking to him about the latest crisis, or just that simple exchange when he'd given her that pot on her birthday, she was content with any conversation so long as it was with him…

Elizabeth almost couldn't believe that this was her; it seemed so… _unlike _her, for lack of any better term. It wasn't like she'd ever been one of those girls who was drawn to the mysterious guy who always sat at the back and never really answered any questions about his past, but there was something about the Phantom… something about his dedication, his courage, his…

Elizabeth wasn't sure _what _it was about him precisely that drew her in, but there was definitely _something _there that made her want to know him more than she did.

It was almost as if- as strange as it sounded- she'd already known him… as if she knew she could trust him because he'd already proven himself…

"Doctor Weir?" a voice said, prompting her to glance up in the direction of the airman who'd just entered the room. "There's been an accident."

_So much for hopes of a quiet trip_… Elizabeth thought, sighing inwardly as she stood up and hurried after the airman.

As much as she liked to hope for the best, even without the fact that nobody would have sent for her if the resulting accident had been minor, living in Atlantis for a year had left her all too aware of the dangers that could be encountered when you left Earth…

* * *

A couple of hours later, as Colonel Sumner sat in silence in one of the laboratories while studying the video that was all that remained to provide them with any kind of information on Doctor Monroe's death, he found himself wondering at what point his assignment to Atlantis had made him more of a police detective and less of a colonel.

Not only did he now have to deal with the obvious problems such as figuring out what could have killed Monroe like that- the doors he was found besides may have all the signs of a short-circuit but at the same time there was no way the doors alone could generate enough power to do that kind of damage-, but even if he solved this before he got back to Atlantis, he still had to sort out the problem of what he was going to do about tracking down the Phantom when he got back…

Actually, that was the main reason for his current problem, really; as much as Sumner _wanted _to still be the same man he'd been before the siege, dedicated to capturing the Phantom for the good of Atlantis before he could do any damage to the city that they were still only just beginning to understand…

No matter how much he tried to remind himself of the dangers the Phantom's way of doing things presented, he couldn't deny that the man's independent attitude hadn't actually hurt them _so _far.

He might have acted on his own rather than cooperating with the conventional military forces on Atlantis during such instances as the nanite crisis or the Genii invasion, but no matter how hard he tried Sumner couldn't think of a _single _way in which the Phantom _could _have cooperated with his men in those instances; on both occasions, the majority of the military had either been on another planet or isolated due to the Atlantis quarantine, making it impossible for there to be anyone available for the Phantom to coordinate with in the first place.

And as for the siege…

The Phantom might have taken charge rather than working _with _them, but given his clearly-demonstrated superior knowledge of the city, it was only natural for him to take control like that; where would the sense have been in having him take orders when he knew more about the city's capabilities than anyone among their forces did?

In a way, he was rather grateful that the current situation was one that he could be certain the Phantom wouldn't be getting involved in- given how far they were from Atlantis it seemed unlikely that the man would be taking part in _this _particular mess, after all-; at least it meant that he could put off dealing with those issues in favour of solving this latest little mystery.

It was just frustrating that the 'mystery' in question was proving to be almost as complicated as the situation with the Phantom in its way. While the burn marks on Monroe's fingertips and the charred door control circuits suggested he'd been electrocuted, McKay had confirmed that the circuits lacked the power to generate enough electrical current to actually _kill _anyone, and the fact that the camera footage of the accident had turned to static _just _at the moment that Monroe was killed certainly suggested something else was going on…

The only question was, what could have caused it? McKay's theory about an isolated power surge had potential, but after spending the better part of a year in Atlantis he couldn't shake a feeling that there was more going on here than he knew…

"Colonel Sumner?" a voice said from the door, prompting Sumner to glance over to see McKay standing there.

"Yes, Doctor?" he asked, pushing himself slightly away from the desk to face the other man. "What seems to be the trouble?"

"Well, I've just been talking to Colonel Caldwell about the whole 'dropping-out-of-hyperspace' thing…" McKay began, looking uncomfortably at Sumner- most likely judging how he'd react to Caldwell being approached before him; Sumner had made it clear to Caldwell that they'd defer to his authority while on _Daedalus_, but some of the Atlantis staff still felt obligated to go to him or Weir first- before he continued. "Anyway, I think Monroe's death wasn't an accident; I checked the power distribution logs against the time code on the security camera, and the only unexplained power spike at the time happened thirty seconds _after _the camera went off, which means that they _weren't_ caused by the same problem…"

"Anything else?" Sumner asked, his year-long experience of the Canadian making it clear to him that there was more to what McKay was saying.

"Well… the fact that Doctor Monroe was working on enabling some computer security protocols when he died _is _a bit suspicious…" McKay said, as he looked uncomfortably at the other man. "I know it sounds crazy, but-"

"You think someone killed Monroe to cover up a problem with the ship," Sumner finished, already standing up. "Has Caldwell stopped the ship?"

"Yeah…" McKay confirmed.

"Good," Sumner said, nodding briskly at McKay as he walked out of the room. "Get to the computer room and see what you and Hermiod can come up with; I'll join you as soon as I've confirmed our position."

_Daedalus _might be the most advanced piece of Earth technology currently in space, but if they were going to remain immobile in hostile territory Sumner would prefer to know what they were dealing with as soon as possible…

* * *

As he strode urgently down the corridor towards the location where the latest accident had occurred a couple of hours later, Sumner couldn't help but wonder how things had come to this; this was meant to be a routine trip back to Atlantis- or as 'routine' as anything like this could be, given that the _Daedalus _had only made this trip once before now-, and here they were with a second death having occurred only two days away from Atlantis and still not even the slightest clue who was responsible for them.

_God_damn_it_… he groaned, cursing inwardly as he recalled what he'd read about the latest death- a technician who'd been helping McKay go over the logs had been sucked out through an airlock when a coolant pipe had ruptured and forced him to retreat in that direction-, _who the _hell _decided that it was a good idea to store the ship's logs near an _airlock?

He was _definitely _going to have words with Stargate Command when he was done here…

As he rounded the corner where the accident had been reported, the confirming nod from Beckett was all he needed to know that McKay was going to be fine before he moved to stand in front of the Canadian scientist.

"I take it this rules out any possibility of an accident?" he asked.

"Given that Lindstrom was about to tell me something about the _source _of the power spikes that killed Doctor Monroe before the leak, I think that's a pretty safe bet, yeah," McKay confirmed.

"Who else would know what you were doing?" Caldwell put in.

"Well, a lot of people knew we were running diagnostics, but nobody knew we were in that particular room at that exact moment," McKay replied, only a slight trace of confusion betraying his concern at recent events.

"Which leaves us with the possibility that whoever's behind this can access the security cameras to erase evidence _and _monitor our investigation…" Sumner mused, before he looked back at McKay. "How many personnel on board have the technical skills to do something like this?"

"Almost everybody!" McKay replied, looking over at Caldwell in only slightly-winded frustration. "That's what you get for assembling a team of brilliant scientists!"

"Well, we've already conducted thorough searches of the _Daedalus _before departing from Atlantis and every day ever since; even without the headcount from the life-signs detectors, there's no way that an intruder could have remained hidden for this long without us knowing it," Caldwell said, shaking his head at that theory before he turned to look at one of his officers. "As of this moment, I want our civilian personnel confined to quarters."

"What?" Doctor Weir- Sumner hadn't fully registered her presence earlier; she'd been standing in a nearby doorway- said, walking out of the door to look pointedly at Caldwell.

"It's the only sensible decision," Sumner said, looking over at Weir with the same stare he'd perfected when discussing the Phantom. "As Doctor McKay just pointed out, there's no way to know who's responsible for what's been happening here; until we can confirm anyone's guilt or otherwise, we have to confine everyone not present at this time."

Even as he walked off with Caldwell to issue the relevant order, Sumner couldn't help but think that he could almost feel the glares of his colleagues from Atlantis practically boring into his back.

He knew they weren't going to like it, but that was the way things had to be; he had to maintain _some _degree of professional detachment if he was going to effectively do his job on Atlantis, and getting sentimental about letting people wander around freely when there was evidence to suggest one of them was guilty of murder wouldn't help that.

Atlantis had enough authority issues with the Phantom's presence alone; he couldn't afford to let attachments cloud his judgement at times like this.

* * *

AN 2: OK, quick appeal for assistance; can anyone think of a good name for a pilot to take John's place in that brief flight to destroy the _Daedalus _communication array?

Just one warning; don't expect to get too attached to the guy…


	5. Stopping the Virus

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Thanks to Infinite Freedom for suggesting the name of the F-302 pilot I used here

AN 2: Hope you guys like my new resolution for the F-302 crisis; it wasn't easy to think up, but I like to think I came up with something plausible

Mystery of the Phantom

An hour later, as Sumner stood on the _Daedalus_'s bridge staring at the computer screen above him, displaying a language that he'd only seen briefly and already knew he'd seen enough of to last him a lifetime, he couldn't help but curse.

"We have a _Wraith _computer virus in our systems?" he said, looking critically over at McKay and Caldwell, uncertain who to berate first; this might be Caldwell's ship, but McKay was the alleged 'genius'. "How did we miss _this_ earlier?"

"In all likelihood it was transmitted in a compressed format during our battle with them," McKay explained. "It probably took a while to reach a point where it could spread to the point where it could affect our systems; we wouldn't have noticed it during the initial check of the computer systems after the battle, and it probably only activated after some kind of trigger event."

"What kind of 'trigger event'?" Sumner asked.

"Possibly the fact that we're once again in close proximity to Wraith territory?" McKay said, looking over at the colonel with an anxious expression that did little to truly express how terrified the current situation must be making McKay feel. "From what I've translated so far, I think it was ultimately designed to take control of the navigational system; fly the ship right to them."

Sumner didn't need to be a scientist to realise the implications of the Wraith getting their hands on the _Daedalus_; with access to the information in the _Daedalus_'s computers, they'd not only learn Earth's coordinates, but they'd also have access to information about how to duplicate the intergalactic hyperdrive technology that Earth had acquired from the Asgard…

"Hold on," Sumner said, looking pointedly at McKay as a thought occurred to him. "I understand why the Wraith would have installed this virus, but that doesn't answer why someone on this ship would kill Lindstrom and Monroe…"

His voice trailed off as an obvious suspect suddenly occurred to him. "Hold on… are you saying…?"

"It was the virus," McKay confirmed. "It's actually simultaneously an elaborate artificial intelligence; it can think for itself, adapt itself to new situation…"

"And protect itself by eliminating anyone who might find out about it," Sumner concluded.

"Can it take over the whole ship?" Elizabeth asked.

"Not entirely," McKay replied, indicating a couple of monitors nearby. "You have to remember that there are hundreds of individual computers on board. A lot of them are interconnected so we tend to think of them as one big machine but that's not really the case. There are dozens of back-ups and redundancies, and some systems – like life support – are deliberately isolated."

"So, you're saying that we don't have to worry about losing our atmosphere," Sumner replied, even if he doubted the virus would go that far; the Wraith would almost certainly want to feed on them after going to so much effort to acquire the ship, even if they kept some alive to interrogate.

"There's that, but you have to take into account that some of the more complex systems like navigation and propulsion require a certain amount of interconnectivity to function properly," McKay continued, almost automatically dampening the brief flare of hope Sumner had felt. "In all likelihood, the virus has spread so far through those systems that to isolate it will make the ship impossible to fly. Until we figure out how to get rid of it, we're stuck here."

Before Sumner could ask for further elaboration, an alarm suddenly started to beep from another part of the control room, prompting the small group to look over at one of the lieutenants.

"Sirs…" the lieutenant said as he looked uncertainly at Sumner and Caldwell- although Sumner deferred to Caldwell's authority, many of the military were still sometimes uncertain who to acknowledge first-, "we just… began broadcasting a distress call."

"What are you talking about?" Caldwell asked, walking over to look at another monitor.

"It just came on by itself, sir," the lieutenant protested. "I'm trying to shut it down, but I'm locked out."

"It's the virus," McKay said, prompting Caldwell and Sumner to look back at him. "That's what I mean about adapting itself to new situations. It doesn't have enough control yet to fly us to the Wraith so instead it's calling the Wraith to us… and right now, we are sitting ducks."

_Damnit_… Sumner growled, shaking his head in frustration.

There were some days when it was _not _worth getting up.

* * *

An hour or so later, Sumner's already-low opinion of the current situation had only decreased. Although McKay had managed to come up with a means of eliminating the virus by shutting down and rebooting the system, that had still left them with the issue of the transmitter array, until Captain Chris Price- one of the _Daedalus_ crew, assigned to the ship after displaying a particular knack for understanding the F-302 operating systems- had suggested the most direct manner of dealing with the problem; destroy the transmitter array in an F-302, which he had just taken out of the _Daedalus _hanger in order to put his plan into action.

"All right, Captain," Caldwell said, going over the latest report one last time as he addressed Price's F-302 over the comms system, "we've evacuated all sections in the vicinity of the array and sealed the bulkheads."

"_Understood_," Price replied simply, his voice betraying none of the anxiety he must have been feeling at this time.

"All personnel," Caldwell added, tapping the necessary buttons to redirect the radio to address the rest of the ship, "brace for impact."

For a moment there was nothing, and then the ship shuddered under a sudden impact that stopped before it could really start.

"What's our status?" Caldwell asked, glancing over at another lieutenant.

"Transmitter is offline," the lieutenant confirmed, shooting a relieved smile in Caldwell's direction. "Distress signal has been disabled."

As McKay and Weir exchanged relieved looks, Caldwell reached over to activate the radio.

"Well done, captain," he said over the radio link, apparently nonchalant about how close they'd come to destruction. "Return to the ship."

"_With pleasure_," Price replied, only to speak again a few seconds later with an uncertain tone. "_Uh… we have a problem; my controls aren't responding_."

"Say again?" Caldwell asked.

"_Well_," Price said, clearly trying to stay calm, "_I'm currently moving further and further away from _Daedalus _at an alarming speed, and I can't seem to turn around_…"

"Oh no…" McKay said, looking over at the others in horror. "I should have seen this coming. The navigational software on the F-302 is compatible with our sublight system, which has _already_ been infected; the virus must have uploaded itself onto his ship."

"Can we transport him out?" Sumner asked.

"That _should _work; those systems are still clean…" McKay said, turning to face his console before a voice suddenly cut in over the radio.

"_OK, _Daedalus_, don't get too worried; I _think _I've got an idea here_," Price said, his voice sounding remarkable calm for the current situation. "_The navigation computer's the only problem; if I can shut down the engine and take the computer offline, I _should _be able to get back to you without any problems_…"

"What?" McKay said, hurrying over to activate the radio in response. "Captain Price, _don't _do that; you'll trigger the virus-"

"_I'm taking the computer off-line, Doctor McKay; the virus can't do anything-_" Price began.

"And you think that thing isn't _prepared_ for something like that?" McKay countered. "This isn't like on _Daedalus_; we can isolate it over _here_, but-"

The sound of an explosion over the radio was suddenly cut off as the radio dissolved into static, leaving the bridge crew staring solemnly around at each other before Sumner broke the silence.

"What just happened?" he asked, turning to look critically at McKay.

"Well…" McKay said, looking around with an uncertainty that suggested he was expecting to be blamed for this, "basically, Captain Price must have assumed that he could shut the F-302's systems down and remove the navigation computer so that he could navigate back to us _manually_… but, given that it takes a few minutes for him to shut _everything _down, the virus must have realised what he was doing and triggered the self-destruct to stop him getting back."

"The _virus _did that?" Sumner said, looking sceptically at the Canadian scientist. "I thought you said this thing was an artificial intelligence programmed to deliver us to the Wraith; why would it _want _to blow Price up?"

"Maybe it figured that Price had shown he'd be more trouble than he was worth and thought that a death like that would demoralise us; I'm a _programmer_, not a psychologist, how am I meant to know how a homicidal virus thinks?" McKay protested, before he sighed and turned back to the console before him. "Anyway, on a somewhat more encouraging note, _we_ can safely shut down the virus's access to the ship's self-destruct systems before we progress with trying to wipe the system here; the F-302 was just quicker because there were less computers for the virus to access for it to get its job done…"

"Forget the explanations," Sumner said, turning to glare at McKay. "A man is dead, Doctor; if you can stop any more of us dying, do it _now_."

* * *

A couple of hours later, as McKay went over the last of the computer files necessary to be backed up and restored, he couldn't stop thinking about Price's death; as much as he might have liked to attribute the other man's death to his own mistake, he couldn't deny that the plan _could _have worked under normal circumstances, but he'd been unable to give Price all the information about what they were actually dealing with- Sumner had ruled that it would be 'demoralising' to know they were up against an AI of this scale and simply attributed their issues to a computer virus that caused malfunctions-, and so Price had taken what seemed like the 'logical' course of action without knowing everything he needed to know…

As he completed the last back-up, McKay pushed those thoughts aside; recrimination wasn't going to help anything now.

"Alright, colonel," he said, activating his earpiece radio to put him back in contact with Caldwell, "we're ready!"

"_Thank you_," Caldwell's voice said, before the radio shifted to allow the colonel to address the entire ship. "_All personnel, this is Colonel Caldwell. Prepare for a full system shutdown_."

After a moment's pause to allow everyone to stop whatever they were doing, Caldwell spoke again. "All right, doctor, go ahead."

Nodding in confirmation, McKay nodded at Hermiod, the Asgard activating the controls on his own console, plunging the ship into darkness for a few moments before he reactivated the systems, the ship lighting up as though nothing had happened.

"_Engine room_," Caldwell's voice said, "_what's our status_?"

"All systems are functioning normally," McKay confirmed with a relieved smile. "No sign of the virus; looks like it worked, Colonel."

"May I suggest we vacate this system? Our current position may well have been compromised."

"_Can you give me hyperdrive_?" Caldwell asked

"That will take longer to get back online," the Asgard replied with his race's usual neutral tone.

"I _can_ get you sublight," McKay added, looking at Hermiod as though he wanted to be sure the Asgard recognised that he'd just accomplished something useful before flicking a switch.

For a moment, as he felt the ship begin to move around him once again, McKay almost allowed himself a moment to believe that all was going well…

Then he studied the information on the screen before him, and realised that that was far from being the case.

"_Damnit_!" he yelled, hurrying over to check Hermiod's console to re-confirm his findings before hurrying back to his own.

"_Engine room_," Caldwell said over the radio, "_what's happening_?"

"The virus; it's back!" McKay answered, studying the computers in a desperate attempt to find out what was going on. "It must have full control of sublight navigation!"

"I thought all systems were _clean_," Sumner's voice said- McKay had almost forgotten that the Atlantis military commander was here, he'd been so quiet-, looking pointedly at McKay.

"They were," he replied, shaking his head in frustration at the information before him. "When we did the reboot there was no sign of the virus; this _shouldn't_ be happening!"

"_Whatever you're doing down there, make it quick_," Caldwell said, his expression as frustratingly grim as ever (Would it be asking too much for them to get a military commander who tried to lighten the mood?). "_Our current course is taking us towards a sun_."

McKay's eyes widened in horror.

"A _sun_?" he repeated, looking incredulously at another console that displayed their current course. "Oh, this is bad…"

"At the risk of repeating myself, maybe we should focus on figuring out _how _this virus is still here after we allegedly wiped it?" Sumner asked, staring in frustration at McKay. "Preferably _before _we crash into the sun you're so worried?"

"That is incorrect," Hermiod said, looking up at Sumner as he studied his own consoles. "A more precise calculation of our heading shows that we will not collide with the star, but rather make a close approach, near its coronasphere. The ship will survive, but the radiation will kill everyone on board."

Sumner could only stare in frustration at the Asgard, but stopped himself actually saying anything; right now he'd probably end up shouting at Hermiod, and the last thing he wanted was to get an Asgard angry at him, even if they didn't seem the type to hold a grudge…

"Why kill everyone if they already _have _navigational control?" Elizabeth asked, voicing Sumner's main question.

"The virus has access to our database," McKay explained. "It knows our tactics, our tendencies-"

"Including the fact that we'd destroy the ship before we let them have access to it," Sumner concluded, groaning as he stared upwards in exasperation, quickly realising what the Wraith had planned. "It's one problem after another…"

_And this time we don't even have our secret weapon_… McKay reflected, not even bothering to chid himself for the lack of logic in having so much faith in a man he still knew nothing about; after saving the city at least four times since they'd arrived there, he thought the Phantom had earned a degree of respect, to say nothing of a great deal of credit for his ability to handle so much crap that not even SG-1 had had to deal with…

"Wait a minute…" he said, snapping his fingers as inspiration suddenly struck him, looking eagerly around at the others. "There was a situation similar to this back at Stargate Command; I remember reading the report. An alien entity took control of the base computer, so they did a systems shutdown to destroy it; it survived by uploading itself into a MALP."

"We don't _have _MALPs-" Sumner pointed out.

"No, we've got a bay full of F-302s," McKay finished. "We already know the virus can upload itself into the ship's navigational computer, but it could have used any one of those ships as a hiding place while we wiped the _Daedalus_ systems clear' it's the only possible explanation."

"So…" Elizabeth asked, looking questioningly at McKay.

"_So_," McKay continued, with a slight smile on his face at the thought, "we physically pull the memory storage modules from the 302s, and then do another shutdown, and _that _should do the trick."

"Right," Sumner said, nodding in resolution at McKay before he glanced over at Elizabeth. "Contact the bridge and fill Caldwell in on the latest development; McKay, you're with me."

* * *

As he hurried through the _Daedalus _corridors towards the F-302 bay, Sumner made a mental note to recommend complete computer analysis be carried out on Earth ships every time they encountered the Wraith; the last thing they wanted was a repeat of this particular mess…

Still, in some ways, he couldn't help but feel a certain satisfaction in the current situation. It might be difficult having to figure out a means of stopping a foe that could use your own ship against you, but at least he could be _sure _that he was solving this crisis on his own; he didn't want anyone to start speculating that he was becoming complacent due to the present of the Phantom to help him out…

Then the door in front of him and McKay suddenly closed before they could go through it, and he knew that the situation wasn't going to be that simple no matter how much he'd hoped otherwise.

"It's not working," McKay said, after his attempts to activate the door from the keypad failed.

"Let's try another way," Sumner said, refusing to consider the worst-case scenario as he led the way down another nearby corridor, only to be cut off by another closing door.

"It's the virus," McKay said, looking nervously over at Sumner after another attempt to activate the door failed. "It must know what we're trying to do."

"Great; a virus that knows what we can do to treat it…" Sumner groaned, shaking his head before he reached up to activate his radio. "Bridge, this is Sumner; are there any open paths to the 302 bay?"

"_That's a negative, Colonel_," Caldwell's voice replied after a momentary pause. "_Looks like the entire section's been sealed off; we've tried to override it but we're not having any luck_."

"Right," Sumner said, nodding grimly as he came to the only conclusion left available to them. "You'll have to beam us in-"

"Wait; _what_?" McKay said, turning to look incredulously at Sumner. "The Asgard beam wasn't designed to beam from one point to another point inside a ship; we could end up rematerialised half inside a wall!"

"Right now, we don't have much of a choice," Sumner said grimly, trying to make it sound like he'd already known that; he had to at least give the _impression _that he was still in control if they were going to get through this. "We'll have to take that chance."

"_Right_," McKay muttered in exasperation, looking up at the ceiling as Sumner moved into position beside him.

"Ready," Sumner said briefly into the radio; McKay looked like he was trying to scrunch himself up for some reason beside him, but the last thing Sumner had time for now was giving a near-hypochondriac a chance to relax even _without _the time limit they were facing.

"_Stand by_," Caldwell replied, McKay crouching down slightly as the colonel spoke. "_Hermiod says we need to make a few adjustments first_."

After another few moments of waiting- during which McKay continued to do what even Sumner would have to describe as an attempted impression of a dwarf-, Caldwell finally spoke again to inform them that the transporters were active, moments before white light engulfed Sumner's vision…

The light faded away almost as soon as it had appeared, revealing the fighter bay around them, along with the full compliment of F-302s.

"It worked!" McKay said, already straightening up as he spoke (Sumner decided not to think too much about the fact that McKay was surprised at that; the man might be smart, but it did him good to recognise that he wasn't right _all _the time).

The Canadian scientist's joy was cut off as alarms and lights began to blare all around them, followed closely by the bay doors at the other end of the room beginning to open…

Sumner didn't need to have any kind of science degree to know that he was _not _going to like what would happen next…

Then he realised that the expected sudden 'fall' towards the doors and he and McKay were sucked out of the hanger along with the air wasn't happening; actually, apart from the doors being open, the hanger seemed perfectly normal.

"We should really, _really _be dead right now," McKay said, confirming that at least Sumner's thoughts about the strangeness of this situation were accurate.

"_Colonel Sumner, Doctor McKay, can you hear me_?" Hermiod asked, breaking the stunned silence that had settled over the two men.

"Affirmative," Sumner responded.

"_I have raised the fighter bay shield in order to prevent the atmosphere from escaping_," the Asgard explained. "_However, the virus has invaded the system and it is only a matter of time before it gains control; therefore, I suggest you complete your task as quickly as possible_."

Sumner didn't need further information; moving as quickly as possible- grateful that he'd attended the briefings on the F-302s while back in the SGC; he might not have been planning on flying them but that didn't mean he hadn't been determined to make sure he knew everything about them that he could-, he hurried towards the nearest F-302 and pulled out its memory storage module, barely registering McKay doing the same as he hurried from one F-302 to the other, leaving the modules in the control chairs as he moved on to the next one; they should be secure enough there and carrying them around would accomplish nothing…

It was just as he reached the last F-302- McKay hurrying over to join him after removing the module from another; Sumner had a theory the scientist just didn't like being alone for too long with the ship in its current condition- that Sumner heard a whistling sound that definitely wasn't something he wanted to hear in this situation.

He barely had time to think before he acted; already crouched down in the F-302's cockpit, he waved McKay into the rear seat before he closed the canopy over them, cutting them off from the rapidly-depleting oxygen supply outside the ship as the F-302's own natural air supply activated.

"…_Sumner, do you read_?" Caldwell's voice said; judging by the tone in his voice, he must have been talking over the radio for a while but Sumner hadn't heard it.

"This is Sumner," he said, taking a couple of deep breaths to regain the oxygen he'd lost before the canopy had closed. "Doctor McKay and I are fine; we managed to get into the last F-302 before we lost atmosphere, and all memory units have been pulled."

"_Understood_," Caldwell said briefly. "_We'll attempt another emergency shutdown now; we'll let you know when it's done_."

With that, the radio communication was terminated, leaving Sumner sitting silently in the F-302 cockpit as he stared patiently at the sight before him. Fortunately the memory modules he'd removed earlier must have been positioned in a low enough location in the cockpits to be caught under the control consoles when he'd removed them, otherwise they'd have been sucked out with the loss of atmosphere, and everything else in the hanger was already bolted or strapped down in the event of such a problem…

"You know…" McKay said, drawing attention to the sound of rapid breathing taking place behind him, "I've never actually been inside one of these before today. It's a little… uh… cramped, huh?"

"Just relax, Doctor," Sumner replied; he didn't have time to pander to the astrophysicist's claustrophobia. "We're safe."

"Great," McKay said, even as the panicked tone in his voice made it clear that the situation was anything _but _great. "Quick question, though, just out of curiosity: how much, uh, air do these things carry?"

"Enough," Sumner replied, his tone a brisk one that allowed no room for argument. "And it'll last longer if you stay silent."

He really wasn't in the mood for another conversation with McKay as the scientist panicked about what might go wrong; right now, confined as they were, there was literally nothing they could do but wait until the virus had been purged from the systems.

A couple of minutes after that last exchange between them, the F-302 bay darkened as the power was shut down, followed by the lights coming back on a few moments later.

"_The system is clear_," Hermiod's voice said over the radio, prompting a relieved sigh from Sumner as the hanger doors closed once again. "_The virus is gone_."

"_Oh_, thank God…" McKay said, slumping back in the chair in relief as Sumner clambered out of the F-302. "At least _that's _over with…"

"Quite," Sumner said simply, shrugging slightly as he looked at the astrophysicist. "So… are you going to sleep in there until we get back to Atlantis, or would you prefer to go back to your cabin?"

* * *

AN 3: Well, it's back to Atlantis in the next chapter, as Elizabeth discovers a _very _interesting clue in her search for information about the Phantom


	6. Meeting Ronon Dex

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Mystery of the Phantom

As Elizabeth sat in her office in Atlantis, she couldn't help but smile at the feel of the reports in her hand; she knew that it sounded a bit arrogant, but after spending so long answering the questions and problems of others, it was a relief to be the one who made the final decisions once again now that she was back in Atlantis.

What made that fact even better, as far as she was concerned, was the fact that the situation in Atlantis had continued to run fairly smoothly since the end of the siege. So far there'd been no apparent sign of Lieutenant Ford or the Wraith, which was at least somewhat encouraging; if Ford had been captured the Wraith would probably have come back to respond to the knowledge that Atlantis still existed, so the fact that there was no sign of them suggested that the resourceful lieutenant was still out there. Zelenka had also reported that a large amount of previously-inactive technology had started to come online after the installation of the new ZPM; with an almost fully-charged ZPM combined with the ten percent still available from their original module, the remaining staff on Atlantis had been able to devote more power to activating systems that had been previously left dormant to conserve the ZPM's energy.

Admittedly, the new soldiers were something of a point of concern for Elizabeth as far as their attitude towards the Phantom went- and she _really _needed to stop thinking about that; he hadn't contacted her so far, but the lack of information about his capture made it fairly clear that he was still out there in the city somewhere-, but she wasn't too worried about it; if her first year in Atlantis had shown anything, it was that John could take care of himself under most circumstances that would have caused anyone else serious trouble…

Her thoughts were cut off by the sound of an incoming wormhole being dialled, prompting Elizabeth to glance up and out of her office just in time for the Stargate to activate, the shield being lowered a few seconds later to allow Major Evan Lorne- one of the new additions to the Atlantis staff and Sumner's new second-in-command- to walk through the wormhole, one of his team close behind him.

Elizabeth's suspicions were instantly on-edge as the wormhole closed with no sign of the other two members of Lorne's team; the casual manner in which he was walking at least suggested that it wasn't bad news, such as the others having been abducted or something like that, but Elizabeth had a feeling that Atlantis's 'quiet period' had just come to an end.

"A dead Wraith that had been shot with _bullets_?" Sumner repeated as he looked at Lorne; he might trust the younger man's record, but getting used to a new second-in-command wasn't exactly easy…

Actually, as much as Sumner hated to admit it- it sounded so _arrogant_ even to himself-, a part of him had preferred Ford because he was younger; unlike the lieutenant who'd served in his position last year, Major Evan Lorne already had a certain way of doing things in positions of authority like this, while Ford had been thrust into the position of command out of a lack of any other high-ranking officers to do the job instead and had been trained based on what _Sumner _was looking for in a second-in-command rather than anyone else.

It wasn't that Sumner had a problem with people doing things their way rather than his way so long as they were properly trained; he'd just grown used to _knowing _how his officers would deal with certain problems, and he no longer had that same certainty any more.

"Yes sir," Lorne replied, nodding in confirmation at the colonel and drawing his attention back to the present; the meeting that he was currently attending with Doctor Weir and Teyla in Weir's office. "At least, it looked like bullets; the guy was a real mess by the time we got to him…"

"The Genii have such weapons," Teyla pointed out, which didn't make Sumner feel any better; with the way things were between them since their attempted takeover of the city, the last thing he wanted was to run into _more _Genii.

"Doctor Beckett is performing an autopsy," Doctor Weir began, only to pause as the aforementioned doctor entered the conference room, looking anxiously around at the others. "And here he is now."

"I'm not done," Doctor Beckett began (Almost before Doctor Weir had finished, Sumner noted; it didn't matter too much in private, but that kind of lack of formality could be problematic if it got out), "not nearly, but I thought you might like to know this; the enzyme sac under the right arm has been removed."

Sumner's eyes widened in understanding.

"_Ford_…" he said, inwardly cursing at what this new turn of events could mean for the young man just as McKay entered the room.

"What's going on?" the Canadian scientist asked.

"If you hadn't been_ late_, you'd known that we've just found a dead Wraith on P3m-736 which all evidence suggests was killed by Lieutenant Ford," Sumner replied briefly, before he turned back to Doctor Weir. "Permission to take a team on a retrieval mission, Doctor Weir?"

"Granted," Doctor Weir replied with a brief nod.

"Whoa, wait a minute; _736_?" McKay repeated, looking at Sumner as though he'd just been ordered to fly. "The UV index there during the day is something like a _thousand_…"

"Bring your sunscreen," Sumner replied; he didn't have time for team members who weren't willing to pull their weight when he ordered them to do so. "Be ready in ten minutes."

With that, he walked out of the office and headed for the armoury, already making a note to prepare himself for the worst-case scenario.

No matter how fond he might have been of the young man back when they'd been cut off from Earth, the fact remained that, with his mental state currently a mess from that Wraith enzyme in his system, coupled with the fact that his condition required him to seek out the Wraith like an addict searching for his next fix…

If things reached a point where he was certain that he couldn't capture Ford and bring him back to Atlantis for treatment, he may have to kill his former teammate to prevent him compromising the base's security.

Sumner would just have to hope that it wouldn't come to that; he had a feeling that Teyla and McKay wouldn't exactly be receptive to the idea of him killing someone they'd worked with for as long as they'd spent time with Ford…

A couple of hours later, Elizabeth continued to go over various forms, signing her approval on various forms involving experiments in some of the newly-activated sections of the city, while making it clear that all scientists involved were to report to a qualified linguist before they even thought about touching anything; Doctor Jackson's absence might be an issue- she still wished she'd been able to persuade _Daedalus _to wait behind until whatever that 'Vala Mal Doran' woman had wanted with him had been dealt with, but she had to admit that she was grateful to be back in the city-, but that didn't mean that the rest of her translation staff were incapable. So far they'd yet to discover anything significantly interesting- the possibility that there might be a way to recharge the ZPMs in particular had inspired a great deal of attempted research-, but there were still some intriguing discoveries.

Zelenka was particularly intriguing by an as-yet-unidentified device he'd discovered in one of the labs near the centre of the city, which seemed to have been damaged the last time it was used; examination of the interior that revealed that many of the control crystals commonly used in ancient technology were badly cracked, with some of them even blackened in a manner that suggested there'd been a fire in the machine the last time it was used. He was still unclear what it actually did, but he had assured her that he would let her know what it was for as soon as he could spare the time to do some more thorough research in the database…

Not for the first time, Elizabeth wished that she'd been able to convince the diplomats in charge of the SGC to allow the Phantom a bit more leeway in his cooperation with the city- rather than the possible unofficial cooperation that Sumner's recent attitude suggested he'd allow to take place in the event of a more serious crisis-; if nothing else, he might have been able to tell them a bit more about some of the technology they were uncovering in their more recent explorations. The group back on Earth might have recommended capturing the Phantom in order to make him talk, but Elizabeth was fairly certain that John wouldn't have much to say in that scenario no matter what they did to him; he did more good while he was free in the city and able to do things his own way than he could ever accomplish locked up or under another's orders, and locking him up might only limit his willingness to help them…

It was almost funny, now that Elizabeth thought about it; what she knew about the man who'd saved her life on at least three separate occasions- he'd specifically saved her during the Genii invasion of Atlantis and had gone on to save the city as a whole during the nanite crisis and the recent siege- was really shockingly little when she studied it closely, and yet, when she got down to it, she trusted him to protect her in a crisis more than she trusted Sumner (Even if she still didn't know _why _he seemed so particularly interested in protecting _her_…).

God, when Lorne had called to request assistance in finding Sumner and Teyla after they apparently vanished during the search for Ford, Elizabeth had briefly thought about asking John to go and help them before she decided against it; from what she'd heard and seen about that planet in reports, there wasn't much more John could realistically be expected to do beyond be another pair of eyes…

But what had prompted her to _do _that in the first place?

What _was _it about John that inspired such… _faith _in her?

Why did she believe that _he _could do something even if nobody else could…?

The sound of the gate dialling pushed all thoughts of John temporarily from her mind, particularly when Chuck glanced over at her in the manner that she'd come to recognise as his 'you've got a message' attitude; clearly someone wanted to talk to her over the radio.

"This is Weir," she said, as she entered the control room and nodded at Chuck to activate the radio once again. "What's your status?"

"_Doctor Weir, this is Colonel Sumner_," Sumner's voice replied. "_No immediate sign of Lieutenant Ford yet, but Teyla and I ran into… someone that I think could be helpful to us_."

Elizabeth was unable to stop the momentary surprise that crossed her face; after Sumner's continued suspicion of the Phantom- he'd only started trusting the Athosians on missions after those Athosians who'd joined offworld teams had been given fairly thorough training in their weapons and tactics-, to hear him say that someone he'd only recently met could be _helpful _to them…

"Who are we talking about?" she asked, deciding to focus on the matter at hand; if this man was good enough to merit Sumner's approval, she wanted to know more about him as soon as possible.

"_He introduced himself as Specialist Ronon Dex; apparently he was culled from his homeworld seven years ago, but the Wraith stopped feeding on him for some reason- he doesn't know why and I'm not inclined to doubt that; he looked as puzzled by it as anyone- and turned him into what Teyla calls a 'Runner'- basically someone the Wraith hunt for sport with a tracking device in them-, and he's been on the run from them ever since_," Sumner replied. "_There's no way to verify how long he's been doing this, of course, but the man definitely knows what he's doing- he took me and Teyla down while we were on full alert before we even knew he was there, and he was able to outdraw me even when I took him by surprise-, and he's offering to help us track Ford if we can remove the tracking device from his back_."

"And… you trust him?" Elizabeth asked, surprised that Sumner was even saying this; after all the times he'd disagreed about having the Phantom in Atlantis, he was now supporting the idea of another alien helping them?

"_Well… I trust that he knows what he's talking about; it might not be our military, but he's definitely had some kind of training, and he clearly _looks _like he can handle himself_," Sumner said at last, before he sighed slightly. "_Besides, he's still got Teyla; I've already lost one of my team, and I'm not that interested in losing another. If Beckett can at least take a _look _at this guy, we might be able to get him to help us out now; we might even have an ally if we can help him make contact with his people afterwards_."

"All right, fine," Elizabeth said, nodding in understanding while trying to seem nonchalant despite her inner satisfaction; it wasn't quite what she was hoping for in a best-case-scenario, but if Sumner was willing to accept this man as an ally than he might be more receptive to the possibility of working with John in the future…

A few hours later, Beckett's impromptu 'house call' completed and the new arrival out of the room where he'd been staying while getting one last check-over, Elizabeth could only wish that she had better news for him. Specialist Ronon Dex of Sateda- Sumner hadn't been kidding when he said that Dex looked like he could handle himself; the man gave the impression of being far larger than everyone else than he actually was, and looked like a pretty formidable fighter even without that impression- might not have been able to help them recapture Lieutenant Ford, but that was only due to the young man fleeing into a Wraith culling beam rather than allowing them to help him (Sumner had been unable to stop him because the unexpectedness of the manoeuvre had caught him off-guard); according to McKay and Sumner's first-hand reports, he'd done exceptionally well in fighting the enzyme-enhanced Ford prior to that.

As he stood staring at the screen displaying the devastated, apparently bombed city on the other end of the wormhole leading to the address that he'd identified as Sateda, not even Dex's seemingly default expression of a grim stare could stop Elizabeth from recognising that she was looking at a man who was barely able to process the fact that he'd just lost everything.

"I… don't understand," he said at last, almost as though he was seeking confirmation of what he was looking at.

"We have machines called MALPs," Elizabeth explained, sparing a brief moment to be grateful that what they'd seen suggested that Sateda had been at least somewhat technologically advanced; what they'd gathered from the MALP suggested a development level maybe a couple of decades ahead of the Genii (Most likely due to the more public nature of the expansion rather than the Genii's efforts to remain secret). "They're capable of transmitting back images and information from other planets. We sent this one to the address you gave us."

"That is Sateda?" Dex asked, his expression making it obvious that he already knew the answer; like anyone having received news like this, he was trying to find other ways of asking the same question to stop himself having to face the reality of what had just been revealed to him.

"I'm sorry," Sumner said, nodding slightly at Dex. "It doesn't look like anyone survived the last attack."

After a few moments of silent staring, Dex turned around and walked back down the stairs, the motion giving Elizabeth a brief glimpse at the weapon that hung by his side-

She froze.

She'd seen that gun before…

It had only been a brief glimpse, but the weapon that Ronon Dex was carrying was definitely _identical _to the gun John had used on Kolya when she'd been held hostage; John's later use of it to disarm Sumner and Everett's men during their confrontation in the conference room before the siege must have happened too quickly for anyone to really make out what it looked like or Sumner would have asked Ronon about the weapon already.

Elizabeth couldn't believe it.

_My first clue_… she reflected, allowing herself a slight smile while nobody was looking.

It wasn't much, of course- given what they'd seen of Sateda it didn't look like the Satedeans had possessed the technology to develop something like that themselves-, but it did give her something to work with; at last she had the chance to get _some _kind of more specific information about what John might have been up to in his life in Atlantis before they arrived, beyond just killing Wraith when they were attempting to cull a planet…

Later on, the day's work completed and her only immediate appointment being with her bed for a few hours of sleep, Elizabeth found herself standing in front of Dex's now-unguarded room- without the Ancient gene and with his planet gone, Dex had nowhere to go, so Sumner had decided to remove the guards from his room-, knocking briefly on the door and hoping that the new arrival wouldn't mind her questions; he might seem somewhat 'rough around the edges', but he otherwise seemed to be a good person.

"Come in," Dex's voice said, turning to face her as she entered his room. "Doctor Weir."

"Specialist Dex-" Elizabeth began.

"Ronon's fine," De- Ronon replied briefly.

"Ronon," Elizabeth corrected herself, smiling slightly at him in gratitude for the informality- she could never get entirely used to military protocol of referring to people by their surnames-, "firstly, I wanted to express my… condolences… for what happened to your world; I know that doesn't make up for anything you've lost, but-"

"It's appreciated," Ronon said briefly.

"Thank you," Elizabeth replied, before assuming a more serious expression. "Secondly, I wondered if I could ask you something."

"If you want," Ronon replied. Elizabeth was briefly reminded of diplomats she'd met who allowed her to make a point without realistically expecting it to make a difference to their wishes, but decided to go for it anyway.

"Where did you get your gun?" she asked, hoping he'd assume it was ideal curiosity and leave it at that; given that Ronon hadn't asked about the Phantom yet, Elizabeth was assuming that he wasn't particularly interested in the man in question and saw no reason to make her own curiosity about the masked man known to him (If nothing else, given that the Phantom had evidently failed to show up to save Ronon's world she had a feeling Ronon wouldn't be a particular fan of him no matter how many other worlds he saved).

"This?" Ronon asked, drawing her attention back to the present as he pulled his weapon out of his holster, allowing her to look at it long enough for her to confirm her initial assessment of it before he put it away again with a dismissive shrug. "Found it on a crashed ship on a planet I visited once; picked up a few power cells for it while I was there as well- things recharge over time if you leave them alone long enough- and I've used it ever since."

"I can understand why you would…" Elizabeth said, nodding briefly at him before she swallowed slightly while looking at him. "Look, I… I know this won't make up for you having… lost… everyone like that, but if you need somewhere to stay now…"

As she trailed off, uncertain whether he was even interested in hearing what she was saying and wanting to observe his reaction, Ronon glanced briefly at his surroundings before he looked back at her with a brief shrug.

"Not sure I'd fit in here," he said simply.

"Actually… I think you could," Elizabeth replied. "From what Colonel Sumner told me, you can definitely handle yourself in a fight; given our own limited experience with the Wraith- we only arrived in this galaxy last year-, we'd appreciate any advice you could give us in fighting them, and we could use someone like you on our side in future."

She didn't mention the main reason she was interested in him staying- that she was hoping he could serve as an example that would encourage Sumner to be more receptive to working with the Phantom in the future-, and was only partly successful in convincing herself that she didn't bring that up because it didn't matter; the reason that she gave for wanting Ronon Dex to remain in Atlantis _was _valid, even if it she had an ulterior motive as well.

After a long silence, Ronon nodded.

"I'll keep that in mind," he said simply.

"Thank you," Elizabeth replied, nodding at him before she turned around and walked out of the room, knowing from his current stance that Ronon had no further interest in talking.

Despite the relatively small victory she'd just won- if she'd won any kind of victory; Ronon still had to make up his mind one way or the other-, Elizabeth couldn't help but feel a certain satisfaction at how that conversation had gone.

One piece of the puzzle about John had fallen into place; he'd acquired his main weapon from the same source as Ronon Dex had.

Admittedly, that could still mean that he'd either discovered the same crashed ship that Ronon had found or that he'd discovered the original homeworld of the people who had created the weapon, but it was progress; now all Elizabeth had to do was figure out how that information fit into the background she was trying to create about her city's mysterious hero…


	7. All the Pieces of Him

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: The events of this chapter take place just after the events of "Trinity"; the episodes themselves happened in pretty much the same manner as they did in the show- with the obvious exception of Sumner replacing Sheppard-, so there wasn't much point in rewriting them

Mystery of the Phantom

As she stood on her balcony once again, staring silently out at the sea before her, a part of Elizabeth's mind chided her for what she was doing; here she was, a full-grown woman, and she was waiting on her balcony like a little girl hoping for Santa Claus to come down the chimney…

Then again, that analogy wasn't _exactly _the same; for one thing, children were always taught that Santa _wouldn't _come if they were awake and waiting for him, while Elizabeth had learned from prior experience that the Phantom would only come for her if she was alone somewhere that nobody could reach her…

Of course, that wasn't to say that she wasn't grateful for the chance to spend these few moments alone; things had definitely been rather stressful over the last month or so. Not only were Sumner's team still trying to adapt to Ronon's presence after he'd decided to stay around- he was unquestionably a good person to have in a fight situation, and he'd definitely proven willing to teach the marines some of his methods of killing Wraith, but there was still a certain tension between him and Sumner given Ronon's only grudging acceptance of Sumner's authority-, but their last few missions certainly hadn't resulted in much in the way of positive discoveries for their war against the Wraith.

The time McKay had spent with Lieutenant Laura Cadman stuck in his head wasn't much more than an idle joke around the base now, but it still had the potential to get on McKay's nerves when it came up, and their failure to form any kind of trade agreement with the Olesians hadn't won them any points back home either.

And as for that nightmarish mess with Project Arcturus…

She sometimes wasn't sure what had left her more frustrated about that whole situation; the fact that it hadn't worked, or the fact that Sumner had overruled her doubts about the project and gone back with McKay to carry it out anyway, too focused on the possibility of perfecting a new weapon to listen to Zelenka's doubts about the technology. It was primarily only luck- Sumner's piloting skills in the gateships were still fairly limited; he hadn't even bothered to take another man along because he'd assumed that the mission would be a straightforward trip to the planet before leaving- and the timely arrival of the _Daedalus _that had allowed the two men to make it out alive; virtually the entire _solar system_ where they'd carried out the tests had been destroyed in the resulting explosion as the weapon detonated…

And she _had_ to stop doing that; as eventful as the past few weeks had been, distracting her thoughts to stop herself over-analysing the reasons for her presence on the balcony would only work for so long.

No matter how much she might prefer to think of her interest in the Phantom as professional, ever since her last meeting with Simon-

"You're slipping," a voice suddenly said from behind her. "Time was you knew I was here _without _me needing to speak."

Elizabeth couldn't help but smile at the sound of the object of her thoughts appearing behind her; stopping yourself from thinking about someone by talking to them might not exactly be a logical way of doing things, but it worked for her, and that was what mattered.

"Well, you know, it's been a while since we've had these little chats; I guess that my 'Phantom sense' is a bit rusty," she replied, allowing a brief, teasing grin to cross her face as she turned around to look at Atlantis's mysterious masked protector, apparently unchanged from the last time she'd seen him, clad in his familiar black clothing and silver mask.

_Phantom sense_? she reflected to herself as she looked him over- he seemed slightly thinner than the last time she'd seen him, but she couldn't be certain; it wasn't like his clothing made it easy to get an accurate picture of what he looked like underneath, what with that cloak covering so much of his body when he was standing still-, unable to stop herself from smiling slightly at the thought; it was such a… _casual_… term, it was nice to know that she could still be somewhat nonchalant after everything that had happened to her since coming here…

"So… how were things back on Earth?" John asked, drawing her attention back to him (A fact that she was grateful for; her thoughts had been about to go to an area she _really _wasn't sure she was ready to explore yet).

"About what I'd expected, really," she replied, shaking her head as she looked out at the ocean before her, knowing without needing to look that John was taking up position alongside her, the windows and doors leading from the balcony back into the main part of Atlantis now inaccessible and opaque from the inside to give them further privacy. "The usual collection of SGC soldiers willing to sign up for their next great mission now that so much of our galaxy has been explored," (She wouldn't allow herself to think about the recent news regarding those 'Ori' who'd apparently begun a new religious crusade; there was nothing she could do about that right now so there was no point in worrying, particularly when she still had to deal with the Wraith in _this_ galaxy), "along with the usual issues with diplomats arguing about the way things have been run here…"

She shook her head in frustration at the memory of those particular meetings. "I know I need their approval to keep this expedition going, but that's one part I _definitely _wish I could do without; they're always so focused on what _they _want that they never seem to think about what the people out _here _could use."

She knew that it was a strange thing for her to say after her long diplomatic career, during which she'd relied so often on her belief in others seeking the same goal as her to dictate her strategy, but after her dealings with ex-Vice-President Robert Kinsey during her brief stint in command of the SGC, she'd had to develop a certain scepticism about others' motives in order to cope in this new world she'd found herself in.

Kinsey…

Quite frankly, just _thinking _about that man left her feeling sick at the thought of how he'd tried to use her as part of his selfish schemes to control the Stargate program. In a way, he was one of the main reasons she'd stopped dying her hair; she'd started doing it in college because she found that people took her less seriously with blonde hair than they did with her natural chestnut-red, and thus tended to underestimate her in negotiations until it was too late, but after Kinsey's attempts to use her she'd resolved to start projecting a more assertive image to stop anyone trying something similar in the future.

"Still," she said, shaking those thoughts aside as she looked back at John, "we made it home in the end; that's what matters."

"'Home'?" John repeated, smiling slightly at her- Elizabeth could almost swear she saw a gleam of joy in his eyes as he looked at her, but the shadows caused by his mask combined with the night lighting out on the balcony made it hard to be sure and it rapidly faded to leave only his usual expression if it had ever been there in the first place- before a more uncertain expression crossed his face. "But…well, I apologise in advance if this is too personal-"

"You've saved my life at least three times, John; I think that gives you the right to ask me _some _personal questions," Elizabeth replied, smiling back at him reassuringly, ignoring the part of her mind that tried to point out to her that it wasn't like her to be this casual with someone when she didn't even know his full name.

"Thanks," John replied, before his expression became slightly more solemn. "It's just… well, I thought I heard somewhere that you had a… boyfriend… back on Earth; I just wondered why he isn't… well, why you didn't decide- why he isn't here?"

"Oh, that," Elizabeth said, briefly wondering how John could have heard about her relationship with Simon before she shrugged that thought aside; given the general lack of news materials from Earth in the first year, it wasn't impossible to assume that someone had brought it up in a casual conversation about the lives everyone had left behind on Earth (The issue of what John had been about to say before he corrected himself was something she decided not to look at in particularly great depth; she didn't know where she expected that line of interrogation to go and wasn't particularly eager to make herself look stupid trying to find out when the reasons he might have changed tracks didn't really matter anyway). "He… well, we broke up, to put it simply; I just…"

She sighed slightly at the memory, inwardly sparing a moment to come up with a decent explanation for her actions that didn't include the central reason for her decision- the last thing she wanted was to discuss feelings even _she _wasn't sure about with the _cause _of those feelings- before she continued speaking. "I… he wasn't what I was looking for any more; I've… what I've seen here…"

"It changes you," John said, his tone a more solemn one than his initial manner; it reminded Elizabeth more of what she considered his 'Phantom tone'- the tone he had used when talking with Sumner and Everett about coordinating the city's defences during the siege- than what she had come to regard as his 'John tone' that he used when talking with her. "What you see here… what you witness people _do _here… what you have to do yourself…"

For a moment Elizabeth thought she saw John shudder slightly under his cloak, but his clothing made it hard to be certain of anything and so she avoided mentioning it; judging by the fact that he stopped doing it almost as soon as she first noticed it, she somehow doubted John would be interested in her offering support…

Elizabeth couldn't help but be surprised at her thoughts; she'd actually considered offering John support?

It wasn't that she was uncomfortable bonding with others, of course- one of her main strengths as a diplomat had always been her ability to see all sides of the argument and come up with something acceptable for all concerned parties (She sometimes wondered if Kinsey's warped mind had twisted that aspect of her personality to assume that she'd take more action that benefited _Earth _rather than continue General Hammond's 'tradition' of making too many decisions that favoured other worlds while leaving them with practically nothing)-, but she'd always tried to maintain a certain emotional distance to prevent herself becoming too attached to one side over another; to feel this… comfortable… about expressing herself to someone when she knew so little about him…

Elizabeth wasn't sure how she should feel about that. Accepting that she might have… _feelings_… for John was one thing, but the implication of her feelings being _that _strong based on so little information about him…

"Sorry about that mess with the Olesians, by the way," John's voice said, bringing her back to the present; evidently he was unaware of the direction her thoughts had just taken, and she wasn't that inclined to be particularly concerned about it. "I visited them once a while back, and it definitely wasn't one of the funnest places I've ever been-"

"You've been there?" Elizabeth said, looking over at the man in the mask in surprise, grateful for a topic that might- however indirectly- help her tackle her own issues about her feelings; maybe once she knew more about John, she'd- she knew it sounded petty, but she couldn't help it; what she was starting to feel was approaching the point where it scared her- get over her feelings for him…

She almost hated to think it- it sounded so childish when she actually thought about it, like a small boy asking for help from Superman when he felt sad-, but she'd grown so used to thinking of John as a selfless hero, who always did everything he could for others, that the idea that he'd gone to Olesia and left the planet in that state was…

In some ways, no matter how slightly disheartening it might be, it was refreshing to know that even he could screw up like that; maybe she was more interested in the image of him as an 'infallible' hero than being interested in him as a _person_ (No matter how pathetic that might sound to her, it at least made a certain sense; she _had _entered this city under a great deal of stress…)

"I _am _only one man, Elizabeth; there wasn't really much I _could _do about the situation at the time, regardless of how immoral I found it," John said, his voice drawing her attention back to him as he stared out at the sea surrounding Atlantis, evident regret and self-frustration in his voice that completely undid any impact his initial statement might have had on her; the fact that he felt that strongly about his failure said more to Elizabeth than any words could. "I hardly had the resources available to make them change their way of life, and they didn't have anything I particularly needed; it was… easier… to leave them for a time when I had a viable alternative to their current way of doing things."

Elizabeth simply nodded at his statement, recognising the inadequacy of any words she might offer at this time; clearly the issue of the Olesians was a topic John was far from comfortable with…

Inwardly, however, she couldn't help but allow herself a brief curse at this latest news; her initial thoughts about how it might have… done _something _about the way she thought about John hadn't helped.

If anything, she now felt _more _sympathy for him, looking at him as he stared out at the ocean before him, his shoulders hunched under his cloak in a classic defensive manner that made it clear that the current topic was something that he took very personally…

It was hard _not _to admire his dedication to do what he could, even when faced with a situation where taking action couldn't really have accomplished anything.

"So," she said at last, trying to draw the conversation onto a less difficult topic, "talking of recent events… did you know about Project Arcturus?"

As soon as she'd spoken those words, she realised that she already knew the answer; who else would have dug those basic graves they'd discovered around the outpost for the five people whom they'd soon determined had been the outpost staff.

"Well, I read a bit about what was being developed there in the files, but I never really spent much time there after my first visit," John replied with a brief shrug; evidently he didn't want to discuss the graves and Elizabeth saw no point in bringing it up if he didn't want to do so himself. "My knowledge of Ancient is relatively limited- I can translate enough to get by in most situations; I know how to understand warning signs telling me _not _to go somewhere, for example-, so I didn't exactly know _what _was going on there, but when I'm faced with something capable of destroying an entire Wraith _fleet _in a facility where it seemed that everyone who last visited there had left the building by dying…"

He looked over at her with a solemn expression. "Well, I wasn't exactly inclined to try anything with what I found there, know what I mean?"

"Trust me, I do," Elizabeth said, shaking her head slightly in recollection at the images _Daedalus _had taken of what was left of that solar system after Arcturus had exploded; even with McKay's protests that the system was uninhabited, the sheer scale of destruction that the weapon had caused was terrifying.

"Not much else I can tell you about the Ancients' old experiments, really," John said after a moment's pause, standing back and flexing his shoulders as though working out some stiffness as he looked over at her. "After the first couple of 'abandoned' facilities I visited turned out to be pretty much dead ends- they always required a greater knowledge of the language than I actually possessed to understand what they were up to-, I decided it was better just to stop wasting time checking them out, since most of the time I wouldn't be able to understand enough of what they were trying to do to work out what might have gone wrong."

"Right…" Elizabeth said, nodding in understanding at John's pre-emptive apology; if they found any other Ancient research facilities out here in Pegasus, John wouldn't be able to give them any advice about what they might find there.

"Well, best be off; any longer out here and someone might get suspicious," John said, looking apologetically over at Elizabeth as he smiled briefly under his mask. "Stay safe, Doctor Weir; it's good to have you back."

"Good to _be _back," Elizabeth replied, smiling slightly at John as he turned around and leapt off the edge of the balcony, vanishing into the shadows of the city below her.

As she looked down towards the buildings below her, even as a part of her wondered where John actually _landed _when he did something like that, she allowed herself a slight smile.

It was still only a minor clue, but she now knew something else about the man known as the Phantom; John knew enough about the Ancients' written language to get by, but he didn't know the _entire _language.

On the one hand, it further ruled out the possibility that John was an Ancient who'd awoken from stasis or something like that- coupled with the fact that he'd claimed a weapon from the wreck where Ronon had taken his own gun; a team sent to that planet had discovered a hollowed-out ship that had apparently been cleared of all its contents, but what little technology remained in the ship was enough for the science team to determine that it was significantly less advanced than the Ancients-, but it didn't leave her any closer to finding out where he'd come from originally.

And- on a more personal level- it still didn't explain why she was interested in _him_, or why he had gone to the trouble of giving _her_ of all people an Ancient shield device…

* * *

AN 2: Hope you enjoyed that chapter; the next one moves into my new take on "Conversion"- "Instinct" was basically the same plot as before-, with Sumner's transformation having a SLIGHTLY different effect on his mentality than it did on Sheppard's…

AN 3: To anyone wondering about the reasons for the reference to Sumner and Ronon having a difficult relationship due to Ronon rejecting Sumner's authority, my reasoning is that Sumner basically expects Ronon to 'work' _for _him, while John only ever expected Ronon to work _with _him; Ronon might have appreciated John's ability to lead after seeing it in action over time, but he resents the fact- even if he won't voice it as he prefers being out in the field where he can continue to fight the Wraith- that Sumner automatically expects to be in charge whatever happens, while Sheppard was more willing to allow others to take the lead if the situation required it


	8. Getting the Bug Out

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Here we go; "Conversion", featuring- among other things-, the first Sumner/Phantom match-up…

AN 2: For practicality purposes, this story begins shortly after the check-up we saw in the opening scenes of "Conversion" when Sheppard- or Sumner, in this case- was brought in after being attacked by Ellia only to show no signs of injury; for practical purposes, everything that happened in "Instinct" was basically the same as it was in the original episode, although Sumner was a BIT less inclined to give Ellia the benefit of the doubt than John was

Mystery of the Phantom

As he walked down the corridors of Atlantis towards his room, Sumner couldn't stop himself from slightly scratching at the mark on his arm where Ellia had apparently fed on him; it was a bit strange that there wasn't any sign of an actual wound despite the blood that had flowed from his arm when she'd grabbed it, but he wasn't really in the mood to question that kind of thing right now.

In the end, whatever had happened to him clearly hadn't been a particularly serious injury; most likely Ellia had just still had some blood on her hand from when she'd thrown Zaddik like that- wait, he hadn't _had _that much blood on him-

Sumner pushed those thoughts aside; reflections on the past weren't helping anything- particularly when they were so irrelevant; he didn't have an injury on his arm that could have been the source of the blood, so clearly there wasn't anything to worry about in that regard-, and he was already frustrated enough with Teyla for getting injured like that; if she'd just been a bit _less _careless, she could have helped him and Ronon take out Ellia a _hell _of a lot quicker…

Then again, he supposed it wasn't exactly anyone's fault; they couldn't exactly have predicted that the seemingly-'tame' Ellia would become _that _dangerous when she was exposed to the Wraith retrovirus, especially when Beckett hadn't yet been ready to test it on a live subject. If nothing else, the dissection of Ellia's corpse- the remains had been brought back to Atlantis with them- should at least give the Scottish doctor more information about what had gone wrong that he could use to correct future versions of the serum, and she hadn't caused any serious damage when she'd gone rampant. Zaddik's death hadn't been a desired outcome to that situation, of course, but it had at least dealt with any ethical issues involving the man wanting the body of his 'daughter' for burial, and the elimination of the 'Daemos' had earned them another potential trading ally…

Shrugging those thoughts aside as he entered his room- it was Weir's job to worry about alliances like that; he just had to keep the men in shape for future conflict-, Sumner shrugged his jacket off and changed into a more comfortable shirt before heading for the workout room.

With the alternatives being either talking to McKay about his latest project or a run with Ronon, given his increasingly lowering opinion of the Canadian- he was still rather annoyed at McKay for the mess he'd made of Project Arcturus; if the man hadn't been so arrogant they might have been able to leave that weapon intact and work out some means of devising a less dangerous version- and his low opinion of the Satedean's personal qualities- the 'Specialist' got the job done when they were in a fight, but the man could _not _take a direct order he didn't immediately agree with to save his life, and his stubborn refusal to at least tolerate Ellia could have provoked her to take the retrovirus early and cost them a valuable test subject-, a practise spar with Teyla right now seemed like the most sensible alternate option available to Sumner right now; at least Teyla was skilled enough to give him a challenge while simultaneously capable of avoiding being seriously hurt if he ended up venting his frustrations on her…

* * *

An hour or so later, Sumner stood opposite Teyla with a casual smile on his face, his 'whacksticks' in his hand and his body in a combat stance as he faced her.

He had to admit, he'd definitely made the right choice in choosing this sparring match over the other options; he was actually having a rather good time right now, as opposed to the usual outcome where these confrontations left him bruised and sore on the floor. Normally sparring matches between him and Teyla tended to be rather uneven- he might have been the more militarily-minded of the two of them, but his greater bulk and muscle strength were actually a disadvantage in a martial art which relied primarily on the user's speed and agility when facing something as strong as the Wraith-, but he'd actually been putting on a fairly good performance this time around.

As Teyla moved in for another attack, Sumner blocked her first few blows before countering with his own offensive, his last blow briefly brushing against her hair as a swift duck was all that saved her from a blow to the head, the Athosian woman shifting her stance to stand up once again in a movement that was almost snake-like in its straightforward grace.

"You are doing… very well, Colonel Sumner," Teyla said, nodding slightly in approval at him as she stood up in front of him once more, the slight panting of her breathing giving away more about Sumner's progress than any words she might have said.

"Thanks," Sumner said simply- it wasn't like he _needed _her confirmation of what he already knew, after all-, before he casually tossed one stick aside, raising the other in a more sword-like manner. "_En garde_?"

As soon as Teyla's eyes had widened in acknowledge of what he was suggesting, Sumner had lunged forward once again, the single stick moving so rapidly from one of Teyla's sticks to deflect the other that it was almost like he hadn't discarded his second one, moving so fast that it seemed as though he was still using both of his original sticks.

Before Teyla could fully process what was happening- _primitive cultures always take time to take in the impossible_, he reflected with a self-satisfied smirk before he even realised what he'd been thinking-, Sumner had struck her in one wrist with such force that she dropped the stick she'd been holding in that hand, following the blow up by striking out at Teyla's throat with such a powerful blow that she dropped the other stick and fell to the floor, clutching her throat and gasping hoarsely as she stared in shock up at Sumner.

She'd always known that Sumner wasn't a peaceful man by any means, but he'd never demonstrated that kind of… _brutality_ in their sparring matches before; if he'd struck any harder he could have broken bones… and what he was doing now… the _coldness _in his stare…

For a moment, Teyla was reminded unnervingly of a Wraith as it prepared to feed…

For a time period that would forever seem longer than it had been long after it was over, Sumner just stared down at Teyla, the coldness in his gaze putting Teyla unnervingly in mind of the Wraith they'd captured over a year ago- the last time she'd been in any kind of prolonged contact with a Wraith; any fights she'd had with them since tended to be long-range thanks to the expedition's weapons-, before it suddenly faded, leaving Sumner looking momentarily confused before he seemed to fully process what he was doing.

"Oh my God…" he said, looking at her in shock, unable to shake the disorientation in his mind; he knew that they'd just been fighting, but for the life of him he couldn't remember what he'd specifically _done _in the last few minutes of the fight. "Teyla? Are you OK? What… what _happened_?"

As Teyla stared up at him, pain and shock in her eyes as she gazed at the man crouching down before her, apparently confused at the sight of her in the condition that he had just reduced her to, she could only wonder what had happened to the man she had come to grudgingly respect- his lack of interest in interacting with her or any of their teammates in any manner that wasn't immediately necessary for them to work on missions together didn't help her get along with him, but he was an efficient military commander- to prompt him to do something like that…

She didn't know what had happened to prompt this sudden shift of behaviour, but Teyla had an unnerving feeling that she wasn't going to like learning what had turned him into the man she had seen before her in those brief moments…

* * *

"So… how is she?" Sumner asked an hour later as he stood in the medical bay, looking uncomfortably at Doctor Beckett; he'd been bringing Teyla to the medical wing when he'd received the message from Doctor Beckett asking him to report to the infirmary, prompting him to move at a somewhat faster rate in order to reach the medical bay, but he'd insisted that Teyla get checked up before learning what Beckett had requested his presence for.

"Physically, she'll be fine," Beckett said, looking grimly at Atlantis's military commander as he sat on the edge of a desk opposite Beckett's own chair, his expression making it clear that he had grim news to deliver. "Give her a few days' rest- and don't have her talk too much; her vocal chords took a nasty knock there- and she should be back to normal soon enough; the problem right now is what made you _do _that to her in the first place."

"Yes…?" Sumner asked, looking slightly scathingly at Beckett, suggesting that he'd already come to his own conclusions on that topic and wasn't particularly interested in them being confirmed or denied.

"Well," Beckett said, taking a deep breath as though trying to prepare himself before he continued speaking, "the good news is, I've been able to determine with some certainty that Ellia didn't drain away any of your life-"

"And that's the best news you had to offer?" Sumner retorted, his eyes narrowing as he looked at Beckett. "What's the bad news?"

"Well…" Beckett said, swallowing uncomfortably, "it _looks _like you've been infected with the iratus bug retrovirus; the one we were working on to turn Ellia into a human-"

"The one that _didn't _do that, you mean," Sumner said simply.

"As I said, the treatment was administered prematurely; she was never _meant _to be exposed to it in its current state-" Beckett began.

"Save the speech, Doctor," Sumner cut in, continuing to glare at the expedition's chief of medicine, clearly unconcerned about Beckett's protests. "The point is, I've been infected with that virus and you don't know what it's going to do to me, correct?"

"Well… yes, really," Beckett confirmed, looking apologetically at Sumner. "I mean, Ellia taking a massive dose of the retrovirus like she did was one thing- we knew it would definitely do _something _to her physiology given her Wraith heritage, seeing as how it was designed to infect her in the first place-, but there's no way to know what kind of effect it would have on a human; I can't even _begin _to guess what's going to happen to you, but if what we've seen of your behaviour recently is any indication-"

"And what's _that _meant to mean?" Sumner interjected, standing up straighter as he glared at Beckett. "I feel perfectly fine-"

"You almost broke Teyla's wrist in a _practise_ session, Colonel; I think that 'fine' is far from being an accurate description," Beckett replied, standing up himself to return Sumner's glare with his own despite his shorter stature. "You're already experiencing significant mood swings, and the wound on your arm healed unnaturally fast; until we know for certain what happened to you, you'll need to check in here every six hours for the next few days until we know for sure you're cleared, and I'm recommending that all 'gate activity be suspended until you're cleared as well."

For a moment, as Sumner stared at Beckett, the Doctor momentarily allowed himself to wonder if it was completely wise to argue with a man in a mental state such as Sumner when he already has his doubts about the man's current condition, but then Sumner stepped back and simply nodded at Beckett in acceptance.

"All right," he said simply. "I'll… see you then."

* * *

As she sat in her office idly tapping away at her latest round of Solitaire on her tablet computer, Elizabeth wondered how her life had reached this stage.

In the past her work life had generally been the dullest part of her life- negotiating treaties might be challenging, but people tended to forget that diplomats didn't often have _that _busy a schedule given that negotiations weren't something that happened every day- while her social life, while never exactly a wild party, had been the more interesting part of her existence, but ever since coming to Atlantis the opposite had been true; she spent more time working and organising reports on fascinating discoveries and research that she never would have been able to even _see _working back on Earth- as fascinating as work at the SGC was, it was, if nothing else, far easier to find something new to study in Atlantis-, but aside from a few members of the senior staff such as Beckett and Teyla- McKay, Ronon and Sumner weren't exactly social people, albeit for different reasons-, she didn't really have any actual _friends_, and the closest thing she'd had to a date was-

Something she was _not _going to think about at this time; the situation with Sumner was _more _than enough complication in her life for her to be dealing with right now without adding her _personal _issues (Particularly when she didn't know what those really were herself) into the equation. Ever since his confrontation with Teyla- apparently Beckett was still debating whether he should have Teyla attend a couple of counselling sessions with Doctor Heightmeyer in case she had any remaining issues from Sumner's attack to deal with, after a man she trusted attacked her like that-, Sumner's condition appeared to be significantly deteriorating, with the original wound on his arm having developed Wraith-coloured scales around it and the scales- according to reports she'd heard from the guards stationed at his door- having already spread to his neck. Beckett's team had managed to develop an inhibitor that kept Sumner's mind from becoming too affected by the transformation, but that didn't stop the physical effects of the process, and his temper was apparently still prone to 'mood swings'.

Caldwell's offer to take temporary command of the military division until Sumner's condition was confirmed either way- if necessary a more permanent replacement would be sent to them from Earth, but all were agreed that they'd only do that if Beckett was certain that it was impossible for them to at least halt the mutation- at least saved her having to worry about issues like that- Major Lorne, for all his training, acknowledged that he was in no way ready to assume command of the military on Atlantis at this time-, but Sumner himself was still a problem. So far the only solution that Beckett's team had managed to develop was the idea of harvesting stem cells from the egg embryos of the Iratus bugs- having discovered a world that was likely to have them using information acquired from the Ancient database- and using them to develop a gene therapy which could repair his damaged cells, but Elizabeth had serious doubts about the likely success of the current mission given what had happened the last time they'd encountered just _one_ Iratus bug, never mind attempting to enter an entire _nest_…

"_Elizabeth_?" a voice suddenly said over her radio earpiece, prompting her to start briefly before she recognised the speaker.

"John?" she said, lowering her voice after a brief glance at her door to confirm that it was locked; it wouldn't exactly look good if someone came in to find her talking to the _Phantom_. "What is it?"

"_Just thought you'd appreciate knowing that I'm keeping an eye on Sumner_," John replied, his own low voice suggesting that he was in a similar position to her in the sense that both of them were trying to avoid being heard. "_Haven't encountered anything _quite_ like this before, of course, but I've heard enough to know what's happening to him; if he tries to get out of that room before you can cure him…_"

He paused for a moment, apparently seeking for the best way to say what he was about to say, before he continued. "_I'll try and take him down in a non-lethal manner, of course- I get that he's not in control of what he's becoming-, but if it comes down to it_…"

"Of course," Elizabeth said, not even questioning the fact that she was saying those words in the first place before they'd crossed her lips. "I understand."

The thing that surprised her most was that she _did _understand. As much as Sumner might still regard the Phantom as a rogue element in Atlantis- a title that Elizabeth was finding increasingly hard to associate with John; everything he'd done s far had always been to their benefit-, Elizabeth had seen enough proof of his dedication to know that John would never do anything that might cause the expedition harm unless he had no other choice, and even then he'd only do it because _not _doing it would cause more harm in the long term. His way of doing things might be more violent than she was used to- the memories of some of the Genii corpses he's left behind him during the siege were proof enough of that-, but even then he'd only attacked proven hostiles rather than going in firing blindly…

In the end, as she terminated the radio connection, _why _she had faith that John wouldn't do any permanent damage to Sumner if he managed to escape in his current condition wasn't important to her; what _was _important was that she was certain that John would keep his word about leaving Sumner alive unless all other options were exhausted.

She couldn't have justified her belief to anyone if they'd asked her, but she _was _certain of it; John had proven himself to her enough times by now, even if others might still need convincing.

She just wished that she felt more optimistic about their chances for ensuring that John _wouldn't _need to do that; she still hadn't heard back from the team they'd sent to the Iratus bug eggs, and the longer it took-

The sound of the Stargate dialling once again prompted her to get up and look at the now-activating wormhole with an eager anticipation, but the sight of Sumner's usual team- now lead by Evan Lorne- walking into the gate room with no sign of Lieutenants Walker and Stevens accompanying them told her and dejected expressions on their faces told her all she needed to know.

The mission had failed.

Two men were almost certainly dead, they hadn't managed to collect any samples of the Iratus bug eggs, and Sumner was _still _mutating…

* * *

As John crouched in a maintenance tunnel just outside Sumner's quarters, his hand hovering near his weapon as he stared at the door before him- Doctor Beckett had just entered the room, but he didn't know what was happening inside it; the doors were fairly secure once they were shut-, he wondered how long he had until Sumner crossed that final line between man and bug.

He couldn't quite believe this was happening; he'd found a surprising amount of information in the Ancient database about Wraith evolution- even if his limited knowledge of the language meant that most of what he'd found there was put together from guesswork-, but the idea that Colonel Sumner was mutating into what could best be described as the Wraith equivalent of the missing link…

He _really _wasn't comfortable with that thought; even if he hadn't heard anything in Beckett's research on the rate of the viral mutation to suggest that Sumner would go so far as to develop Wraith feeding organs, insects were ruthless enough to their own kind. If Sumner's mutation progressed far enough that the inhibitor couldn't keep him lucid- something that even _Sumner _seemed to be afraid of, judging by his earlier request to one of the nurses that had gone in to check on his progress to double the guard at his door-, the potential damage that he could do if he escaped into Atlantis…

Sumner probably wouldn't possess the intellectual capacity to actually do any serious damage to the city if he left his room- if he'd regressed far enough to even _try _to escape it seemed a safe bet he wouldn't exactly be in control of himself-, but that wouldn't stop him from hurting others if he found them. Add in the fact that the trip to the Iratus bug homeworld had- judging by the grim expression on Beckett's face when he'd entered the room- not gone exactly well, and he wouldn't be surprised if-

The sight of Sumner walking out of his room, his eyes now yellow-irised with slits for pupils, the skin around the lower part of his face a bluish-grey colour with small ridges spread around his neck and jaw and his hands in a similar condition with long fingernails was all the confirmation John needed; Sumner had snapped.

Even as the colonel lashed out at the marines on either side of the door, knocking them unconscious with a couple of quick blows, John was already crawling down the maintenance tunnel to the nearest exist, already checking his 'life signs detector' to confirm that Sumner was heading in the expected direction.

As soon as he'd left the maintenance tunnel- the entrance was a few metres down the corridor in the opposite direction from which Sumner had been heading-, John had turned around and began to hurry down the corridor, the detector already modified to distinguish Sumner's now-unique physiology from the humans around him (After all the time he'd spent programming the sensors to _not _register his presence his first few years in Atlantis, modifying them to highlight one specific person was fairly simple). He had to be careful not to go too fast in case Sumner heard him at first, but as he approached a large area that he suspected had previously been the Ancient equivalent of a storage room he quickened his pace; at least there he'd have enough space to start shooting without giving Sumner anywhere to hide…

As soon as he'd rounded the corner and found himself at the top of the stairs leading down to the storage area, Sumner half-way across the room floor and approaching the other exit, John didn't hesitate; drawing his gun, he set it to stun and fired it at the colonel-

The other man ducked to the side and turned around to glare at him, a resolute expression on his bug-like face that seemed to twist into a slight glare as he took in the cloaked figure standing at the top of the stairs.

"OK… Sumner?" John said, trying to sound calm as he stared at the man before him, his hands raised in a reassuring gesture; he didn't know how far Sumner's mind had regressed, but maybe if he just stayed calm Sumner wouldn't recognise him as a threat until he was close enough to knock him out with a stun blast. "I know that you're… having trouble… with what's happening to you, but if you just-"

Before he could say any more, Sumner's eyes narrowed and he charged towards his opponent, hands outstretched as though aiming for John's neck. Whether it was just the bug in Sumner reacting to a potential threat or whatever was left of Sumner in the bug's mind responding to his still-present issues with the Phantom's presence in the city- John had never fooled himself that Sumner had started liking him more after the Siege; he just tolerated his presence better-, John didn't know, and right now he couldn't spare the time to find out; raising his gun, he fired off another stun blast, only for Sumner to duck to the side before he knocked the gun out of John's hand, his own subsequently closing around John's neck.

_Crap_… John muttered, glaring back at Sumner even as the other man began to tighten his grip around John's throat, his left arm pressed against Sumner's throat to hold him back as his right hand tried to find his lost gun. This _isn't good_…

Even without his previous promise to Elizabeth that he wouldn't kill Sumner unless he was certain that it was necessary, his options right now were limited, and his promise just made things _more _tricky. For a moment he was tempted to just forget his word and kill Sumner anyway- he could definitely claim self-defence-, but pushed that though aside at once; even if Elizabeth already saw him as a monster, he would _not _go so far as to _kill _someone in Sumner's condition unless he was _genuinely _certain all alternatives were exhausted.

Right now, his best chance seemed to be to hope that Sumner's healing was as advanced as it had seemed earlier, and throw him off with a quick sneak attack…

John didn't stop to think; as soon as the idea had occurred to him, he ceased his frantic search for his gun and flicked his wrist, activating one of the small knives he kept stored up his sleeve, before ramming the knife into Sumner's side, sending the hybrid staggering backwards in pain. The blow merely penetrated his chest without actually damaging anything vital, but the pain it caused was enough to send Sumner staggering backwards, letting out a bug-like hiss of pain before John used the momentary distraction to draw his gun and hit Sumner with a quick couple of stun blasts, sending him collapsing to the ground.

Taking a brief glance around to make sure there was no sign or sound of anyone else approaching, John quickly hurried over to pull the knife out of Sumner's side before he turned around and ran back down the corridor towards the maintenance tunnel he'd crawled through previously.

Hopefully, anyone finding Sumner would be too grateful that he'd been subdued to focus on how it had happened, particularly when his mutation- according to what John had overheard while spying on the medical bay- only had a few hours to go before it had run its course…

* * *

As she stood at the door of the commissary, looking at Sumner's team as they sat around a table, Elizabeth tried to place what about that picture was bothering her. It wasn't the lack of Sumner among the group, she knew that much- Sumner had barely bothered to spend much time with the team outside of missions even when Lieutenant Ford had been a member, and he'd spent even less time with them now that he was the only official military member of the group no matter how much training Teyla and Ronon possessed-, but there was something missing…

Then she realised what was bothering her.

It was the _lack _of concern about them.

It wasn't that the three people sitting before her _didn't _care about what happened to Sumner, and they definitely didn't _want _him to die; she just got the impression, as she looked at them sitting around the table, that they wouldn't be that bothered if he didn't live either.

Unlike when then-Colonel O'Neill had been infected by the Ancient knowledge and faced a complete mental breakdown, prompting the rest of SG-1 to do virtually everything they could to figure out a way to help him- or even just spend time with him before he reached the point where he couldn't understand what they were doing-, right now Sumner's team weren't even discussing what they _might _be able to do to help him; Elizabeth had a feeling that the only reason they were sitting here was because they weren't sure what else to do.

That was the problem with Sumner's method of leadership, really; it wasn't that he saw the soldiers under his command as expendable, but he didn't make that much effort to connect with them either…

Finally giving up on her own private reflection, Elizabeth walked over to join the team, smiling briefly at them as she sat down at the table with them.

"You guys are up late," she said uncertainly.

"No idea what else to do," Ronon said briefly. "I'm not good at sitting still."

"Well, what _can _we do?" McKay sighed. "The bugs aren't going to let us in, Sumner's reaching the point where he'd probably only recognise us as food if we _did _see him, and I just… just…"

He groaned as he leant back in his chair, staring in frustration at the ceiling. "I just can't help feeling like crap because I can't feel that _bothered_…"

"You are not the only one, Rodney," Teyla said, looking reassuringly over at her friend as she reached over to place a brief, comforting hand on his shoulder. "Colonel Sumner is a good leader, but he… he does not make it easy to care for him beyond that."

Elizabeth said nothing, but secretly she had to agree with Teyla's statement. It might not be something she could really legitimately complain about, but Sumner's distance from the rest of the staff made Atlantis somehow a less relaxed place than the SGC had seemed during her visits there after General O'Neill had assumed command; in many ways, it reminded her of…

Elizabeth sighed slightly, inwardly cursing at her own realisation.

In the end, Sumner's attitude towards the rest of the expedition wasn't that different from the way she'd initially been when she'd arrived at the SGC; professionally respectful of everyone, but otherwise emotionally distant.

The only difference was that she'd made an effort to change that stance after witnessing the bond between the various members of SG-1 as they fought to find the Lost City and save Colonel O'Neill's life.

Sumner, on the other hand, didn't seem that interested in making any kind of change to his attitude towards the others, and there was really nothing Elizabeth could legitimately _do _to encourage him to change it; so long as he was doing a good job keeping the city safe, why would the IOA care if he wasn't much of a people person…?

"_Doctor Weir_," Beckett's voice said over the comms, cutting off further thought in that regard, "_I need to speak to you immediately_."

* * *

As he crouched in a maintenance tunnel just outside the infirmary a few hours later, John allowed himself a brief smile as he heard Beckett's report that his attempt to treat Sumner's mutation had finally proven successful; the man might still have a while to go before he was back in his full human form, but his DNA was reverting to normal at last, which was a definite step up from the state he'd been in before.

The strategy they'd used had been risky, of course- relying on Sumner _himself _to get the embryos necessary to reverse his current transformation could have backfired in so many ways he knew he'd have felt extremely uncomfortable making that decision in Beckett's place-, but given that it had paid off, he supposed everything had worked out for the best…

It was definitely something he'd need to work on, though; he'd spent so long with only himself that he still sometimes felt uncomfortable relying on others to do anything, even when he knew- such as with the Atlantis expedition- that they could handle themselves in a situation without his help (Even if his aid _had _been helpful when he'd offered it; as much as he knew Elizabeth wouldn't have selected anyone to join the expedition if they weren't capable of contributing something to the team, the fact remained that he had little doubt that the nanite crisis and the Wraith siege of Atlantis would have resulted in more deaths than had actually taken place if he hadn't been there).

Right now, though, with Sumner on the road to recovery- no matter how long that particular road was destined to be- and no particular reason for him to be anywhere, it was probably best for him to get back to his old hiding place before the search for him resumed in earnest once again…

AN 3: Hope you all enjoyed that; the next chapter analyses the events of "Aurora" with Sumner the one in command rather than John, as we observe a _crucial _difference in his method of interacting with his team compared to the man we know…


	9. On to the Aurora

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: As promised, my alternate take on "Aurora", beginning with the group congregating in the control room after McKay announces his discovery of the "Aurora"'s signal

Mystery of the Phantom

"What is it, Ro- Doctor McKay?" Elizabeth said, automatically amending what she was about to say as she noted Colonel Sumner standing off to one side of the control room; his recent near-transformation into an Iratus bug hybrid had almost made him more rigidly adhered to the command structure than he'd been before, as though he was trying to escape the memory of how rapidly he'd lost control by enforcing control where he could.

She was trying to encourage Sumner to talk to Heightmeyer about it- her recent conversation with Ronon and his comment about their differing methods of dealing with the Wraith had left her more than slightly concerned about the possibility of the Satedean leaving them, and the last thing she wanted was to give the man who was possibly their best 'official' fighter against the Wraith more reasons to leave due to disagreements with the commander-, but so far she wasn't having much luck; the fact that his military duties hadn't actually suffered as a result of his new attitude meant that she didn't even have a valid reason for wanting him to attend the appointments.

"_That_," McKay replied, indicating a green dot on the main scanner screen behind him that appeared to bee sending the usual 'ripples' associated with the visual depiction of sound waves, "is the signature of an Ancient ship called the Aurora. With the ZedPM now powering the city, we've been reactivating dormant systems; that one tracked the location of Ancient ships during the war."

"A warship?" Sumner asked briefly.

"Uh… yeah," McKay confirmed, the brief gleam in his eyes suggesting that he'd been about to make a joke before he thought better of it (Another reason for Elizabeth not to like Sumner; he rarely seemed to allow people to be themselves), before he walked over to another, smaller screen. "Anyway, I cross-checked the logs. They were on a reconnaissance mission. When we activated the ZedPM, the city must have sent out some kind of an automated subspace beacon recalling ships back to Atlantis."

"How long before it gets here?" Elizabeth asked; no matter what state it might be in after being abandoned for so long, the possibility of looking at an actual Ancient ship was _incredible_…

"Well…" McKay said, as he turned around and began to type on the console below the screen, studying the information before him intently, "given that it's at the edge of the Pegasus galaxy, let me see… carry the four…"

He shrugged dismissively as he turned around to look at the others. "Forty-two million years; should we go wait on the porch?"

"Alternatively," Sumner said, his eyes narrowing as he studied McKay, "we _could _take a gateship through the nearest Stargate to check them out..."

"Unfortunately, as effective as that would be, there aren't any Stargates in the area that we could use," McKay said, his tone only slightly apologetic as he looked at Sumner, clearly enjoying being able to contradict Sumner in secure knowledge that the other man could say nothing to counter his claims.

"Which," Elizabeth reflected as she looked over at the other members of staff in the room, "leaves us only one way to get there."

She was just grateful that it was _Daedalus_'s supply week; the last thing she wanted was to have to wait for the ship to arrive when they had no way of knowing if the Wraith were going to be able to detect that signal just as they were...

* * *

A few hours later, with the _Daedalus _on route to the system where the Ancient ship had been detected- Sumner's team had all insisted that they be allowed to go on the mission, even if Sumner himself had been content to leave it for Caldwell's crew to handle until McKay had convinced him that their superior expertise with Ancient technology would be vital in such a valuable matter-, Elizabeth finally allowed herself to depart her office and head out to her balcony, passing off her destination to the rest of the staff in the control room as a need for fresh air.

As always, she barely had to wait for more than a few minutes before she heard a slight sound on the ground behind her, and knew that the man she was waiting for had come to visit her.

"You're slipping," she said, smiling nonchalantly as she turned to look at John as he stood behind her, a slight grin on his face under his mask. "I actually _heard _you that time..."

"Maybe I let you hear me," John replied, as he walked over to take up a position beside her.

"Or maybe I'm just getting better?" Elizabeth countered nonchalantly.

"Either works for me," John replied- Elizabeth couldn't help but feel touched at that; for a man who spent his life trying to hide, the fact that he didn't mind the possibility that she was aware of her was rather comforting-, leaning against the edge of the balcony before he turned back to look at her. "So, what prompted you to seek out this particular rendezvous?"

"The Ancient ship we recently discovered," Elizabeth replied.

"Oh, _that_," John said, nodding in understanding. "Well, it's not that much-relatively speaking-, but I can assure you that I have no reason to believe there's anything dangerous on the _Aurora_; I spent a bit of time reading some of the Ancient records of the last years of the war, and what I read about the ships from that area doesn't suggest that there was any kind of viral research-"

"Viral research?" Elizabeth repeated, turning sharply to look at John. "The Ancients were experimenting with biological warfare?"

"I never _found _anything about them doing something like that in the records I read; I just said that because it's the only thing the Ancients might have been experimenting with that could still be dangerous to people even after all this time if it was contained on a spaceship," John explained, looking apologetically at her. "The point is, from what I could gather from the logs, there's no reason to believe that the ship is anything other than an Ancient warship that ended up drifting around out there after the war ended; I just can't give you any more information because I don't _have _any."

"I see," Elizabeth said, nodding briefly at John before the two settled into a brief silence until she turned to look at him, hoping her discomfort wasn't as obvious as she felt it was; this was the first time she'd ever asked him something on this topic, but at the same time she felt that it was time to try and broach this topic. "Actually, that brings up something else I wanted to ask you about; why... didn't _you _investigate the _Aurora _yourself?"

John simply stood in silence for a moment, the expression on his face under his mask briefly leaving Elizabeth uncertain if he was going to answer the question or simply jump off the balcony and bring the conversation to a premature end, but then he finally nodded slightly- such a small gesture that she probably would have missed it if she'd had less experience at reading body language than she naturally possessed- and turned back to look at her.

"Well... I tended to limit how much equipment I activated in Atlantis to the things that I was _certain _I knew the functions of- and even then I only turned them on when I actually had some use for them; I wasn't going to start wasting power on something when I couldn't see a use for it and I needed to maintain the city shield while underwater-, so I didn't actually _know _the _Aurora _was out there before you found it yourselves," John explained, looking slightly uncomfortable as he spoke for reasons Elizabeth couldn't entirely work out. "I read about it and a few other ships in the files, as I said, but I didn't know it still existed; for all I knew it had been destroyed during the last days of the war..."

"I see," Elizabeth said simply, noting another point in her private 'file' on John's past; his knowledge of Ancient technology might be impressive, but it evidently was far from limitless. "So... what you know about Ancient technology, you learned through... trial and error?"

"And based on careful study of the Ancient language based on an initially basic knowledge of it; don't forget that," John said, his tone slightly jocular before his face almost appeared to close up as he processed what he'd just said.

"John-" Elizabeth began, curious for more information about his last statement

"Gotta go," John said suddenly, hauling his feet up on to the balcony before he glanced back at her, his cloak hanging down around his body while his feet rested on the railing. "Good luck with the _Aurora_, Elizabeth; sorry I can't be more help to you."

"John-!" Elizabeth began again, only for John to leap out of view before she'd even finished the first word of her sentence, vanishing into the shadows of the city buildings around her before she could properly react.

_Damnit_... she thought to herself, hoping that she hadn't pushed him too far with that last query; the last thing she wanted was to push John away when she still had so much more she wanted to learn from and about him. More than his Ancient knowledge- no matter how limited _he _apparently thought his knowledge of Ancient technology and language might be, what he'd displayed so far was definitely enough to impress her-, John himself represented a mystery she keenly wanted to explore, learning more about where he'd come from and the events that had shaped him into the man he was...

She just wished she knew _why _those details were so interesting to her; was it just because knowledge of the Phantom's past might encourage the SGC to be more open to the possibility of future collaboration with him, or did she want to know simply because _she _wanted to know?

The more she learned about John, the more she found herself uncertain why she wanted to know these facts in the first place...

* * *

As he walked through the silent corridors of the _Aurora_- he'd ordered the team to split up and search the area independently after life support had been activated; the general lack of active life readings made it fairly clear that the ship was safe-, Sumner was starting to feel increasingly uncomfortable with the current mission; as if their earlier close call with that Wraith ship hadn't been enough of a complication- they might have easily destroyed it, but one Wraith ship could easily lead to more if they weren't lucky-, when you added in the fact that there were a bunch of Ancients being kept in stasis pods on a ship where they'd only just managed to reactive the life support systems a few minutes ago, he was starting to feel increasingly like he was on a ghost ship from classic gothic fiction...

He wasn't sure if he felt better or worse now that life support was back up and running; the spacesuit might have offered a certain extra degree of protection, but that didn't totally compensate for the restricted movement and fundamentally enhanced combat vulnerability it offered (Particularly when the Wraith's abilities in airless environments were unknown; there was still some debate about how long the Wraith could last without oxygen or how they might cope in an airless environment).

So far, however, this entire trip was rapidly beginning to seem like the greatest waste of time since their trip to Dagan only to learn that the 'Phantom' had already taken the ZPM that the Ancients had left there for himself; the ship was a wreck, the crew were nearly dead, there was no way to know if there was actually anything _useful _in its databanks...

"_Colonel Sumner_?" McKay's voice suddenly said over his radio, drawing his thoughts back to the present.

"Yes?" he answered briefly.

"_I've just completed my scanning of the stasis pods, and... well, I'm reading cortical signals_!" McKay replied, in an enthusiastic tone that meant nothing to Sumner.

"Which means?" he asked, hoping that whatever had made McKay so excited would at least go some way towards making this trip worth the effort.

"_Basically, the pods have all been equipped with neural interfaces indicating brain activity as though the Ancients were fully conscious_," McKay explained. "_If all of these pods are interconnected, it's highly possible these people are, in fact, communicating with each other_."

Sumner blinked.

There was no _way _he'd just heard that correctly...

"Are you saying... these Ancients have been talking to each other via some... mental network... ever since they went into stasis?" he said incredulously. "But... wouldn't that have been at the end of the war?"

"_Well, it would have been an effective means of keeping their minds occupied until they were rescued, but what I'm seeing suggests that the interface was only reactivated when they detected the recall beacon from Atlantis_," McKay explained. "_Anyway, the neural feedback loop is incredibly active_."

"Is there any way that we can find out what they're saying in there?" Sumner asked, hoping that he was right and McKay actually had a reason for bringing this discovery to his attention in the first place; the concept of the neural network was interesting, but it didn't actually serve much of a practical purpose on its own.

"_Well, that's what I really called you about_," McKay answered. "_We found a couple of empty stasis pods that we could use to link one of us up to the network, but I... well, I thought you'd prefer it if we updated you on the situation before we did anything_..."

"Good call," Sumner said, as he turned around and walked towards the area where he'd previously sent McKay. "Get everything set up; I'm going in there."

He might not be the most scientifically-based member of his team, but he was the team leader; if they were going to make contact with Ancients, it was his responsibility to do so.

* * *

"Hold on; _you _want to do this?" McKay said, looking incredulously at Sumner.

"As team leader, part of my responsibilities do include officially making contact with the worlds and people we visit; the potential importance of this encounter makes adhering to that procedure all the more vital," Sumner pointed out, folding his arms as he glared at McKay. "The fact that you're volunteering to go into that network yourself confirms that it's safe to access; leaving you out here is simply practical sense in case something happens that nobody was expecting."

"It won't!" McKay said in protest.

"But if it does-" Sumner pointed out; looking back, he had to admit that it was a rare occasion when a plan based on McKay's scientific expertise ended up going completely according to plan.

"It _won't_!" McKay protested, his apparent traditional fear of danger pushed aside in favour of defending his scientific expertise. "How many times do I have to say this?!"

"Rodney," Teyla added, in her usual diplomatic tone- for a woman from a relatively primitive society Sumner was often impressed at how well she'd fallen into her unofficial role as their 'liaison officer' for some of the less advanced societies they'd discovered-, "between the two of you, if something _were _to go wrong, which would be the greater loss?"

"Well," McKay said after a moment's pause, apparently missing the glare Sumner shot Teyla as she stared nonchalantly back at him, "I've never thought of it that way, but..."

He glanced over at Sumner. "She's right; _you _should go."

If it wasn't for the fact that her 'deception' had allowed him to get what he'd been after in the first place, Sumner would have made a mental note to have a talk with Teyla and McKay about undermining his authority while in potentially hostile territory; as it was, he simply handed his excess gear to Ronon and laid down in the pod that McKay had just opened for him.

"Assuming I decide to leave, how does that feature work?" he asked, glancing at the Ancients lying in the pods around him; he'd read enough reports about encounters with brain-manipulating technology that had been encountered back in the Milky Way galaxy to know that he couldn't be too careful.

"Well, it's simple enough, really," McKay explained in the manner that always left Sumner feeling like McKay thought he'd just asked the equivalent of how to fit the cubes into the holes on a child's toy. "Once you're plugged in, the system creates a direct feedback loop between the processor and your brainwaves, so when you want to disconnect, you just need to... well, concentrate."

"In other words, when I want to get out I have to _think _about getting out," Sumner stated briefly.

"Well, you'd probably need to _specifically _think about it in order to prevent yourself from popping in and out every time it crosses your mind, but otherwise... yeah, you've got it," McKay said, nodding briefly at the colonel before he indicated the control console in his hands. "Now, I should be able to monitor your EEG patterns, so in the highly unlikely event that something anomalous should present itself, I should be able to, uh, disconnect you manually-"

"Good," Sumner said as he laid back in the pod, looking briefly and pointedly at McKay as he waved a prompting hand. "Let's get on with this."

"OK," McKay said, swallowing slightly in the face of Sumner's glare as he moved to stand alongside the pod. "Now, when I close the lid, the pod system should activate. Ready?"

"I've been ready for the past few _minutes_, Doctor McKay," Sumner said, looking over at the scientist in frustration. "Just get on with it."

"Uh... good," McKay said, tapping on his laptop and sending the pod back into its 'booth', leaving him, Teyla and Ronon looking silently at the now-seemingly-unconscious colonel as he entered the virtual environment.

"Well," Ronon said after a moment's silence, glancing back over at Teyla and McKay, "since that's done, better get back to work; still got a lot of this thing to search."

McKay wasn't sure what struck him as more depressing; the fact that Teyla and Ronon were so quick to abandon Sumner to lie around in a pod where he might not even be able to accomplish what he'd set out to try and achieve, or the fact that he himself was only sticking around because he didn't want to have to deal with the arguments he'd have to put up with if it became public that he'd left his team leader behind.

In the end, it was pretty much what he'd said to Elizabeth during that whole crisis with Sumner mutating into a bug; he just couldn't bring himself to feel that bothered about Sumner beyond a professional capacity. Elizabeth and Carson had been good friends even before they'd arrived there, Teyla was fairly easy to talk to once you got on a comfortable topic for both parties- she tended to just walk away when he talked _to _her about stuff, but some of her insights into the cultures they'd just visited were rather interesting-, and even Ronon wasn't that bad- the man might not really socialise with people that much, but at least he gave the impression that he might miss you if you died-, but Sumner actively seemed to avoid anything that wasn't involved with training or preparing for the next mission or going over how you'd screwed up on the last one...

Quite frankly, McKay was starting to realise just why Carter, Jackson and O'Neill had gone to such extreme lengths to get Teal'c back; if you were going out into the unknown wonders of the galaxy, you felt more comfortable to have someone at your back that you _knew _would save your life because they wanted to do it, rather than just someone who was there to do the job.

Shaking those self-analytical thoughts aside, McKay sat down against the pod, laptop in one hand and gun in the other in case the situation turned ugly, and waited for something to happen.


	10. Failure to Launch

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Sorry about the delay; it was _not _easy figuring out some of the fine details here

AN 2: Advance warning; I won't be covering the scenes in the simulation, but an explanation of what happened to Sumner while he's in there WILL be provided, I assure you

Mystery of the Phantom

After a few moments of waiting, during which he had accessed the ship's databanks just enough to determine that the ship's supply of drone weapons had been depleted at some point, McKay was just beginning to contemplate humming "99 Bottles of Beer on the Wall" as a means of passing the time- trying to solve complex equations in your head might be more intellectually challenging, but at least with "99 Bottles" you knew that you were doing things the right way; without something to write on you tended to forget what figures you'd started out with-, the pod opened up and Sumner emerged, looking over at McKay in frustration.

"Was there anything about this simulation you forgot to tell me, Doctor?" he asked, glaring at the Canadian as he sat up and turned around to exit the pod.

"Uh... no, not really; why?" McKay asked uncertainly.

"Well, beginning with the fact that the Ancients in there don't even appear to be aware that they're _in _a simulation in the first place, I think it's safe to say we have more than a few problems," Sumner said, staring grimly at the scientist.

McKay blinked.

"They don't know?" he repeated uncertainly. "I mean, it's _possible _that the time they spent completely unconscious while the system was shut down could have resulted in them losing some of their short-term memories leading up to them originally going into stasis in the first place, but you'd think that the computer could compensate..."

"Evidently, it didn't; we have more important issues to focus on right now," Sumner said, before he reached up and activated his radio. "Sumner to Caldwell."

"_Caldwell here, Colonel; what's your status_?" Caldwell's voice replied.

"Well, we've gained access to an Ancient virtual reality system that's keeping the crew of the _Aurora _alive, but unfortunately the Ancients themselves don't appear to remember anything about what happened to them to force them to enter stasis in the first place," Sumner explained. "I just got out of it myself, but all I accomplished during my time there was getting thrown into a cell; the entire crew are convinced that they're carrying out hyperdrive modifications to get the ship back to Atlantis faster while the war against the Wraith is still taking place, and simply dismissed me as a spy and had me thrown in a cell before I could convince him otherwise."

"_I see_," Caldwell said in response. "_Well, unless we can find any drones over there_-"

"There aren't any," McKay cut in apologetically. "I checked the records for the ship's armoury while Colonel Sumner was in the stasis pod; they depleted all their drones in their last major engagement before they went into stasis."

"_Right then_," Caldwell said resolutely. "_In that case, there's no reason for us to be here; contact your team_-"

"Actually, there is something we could use," Sumner interjected, cutting Sumner off mid-sentence with a resolute tone (McKay was briefly surprised at Sumner's interruption before reminding himself that Sumner and Caldwell were both colonels and hence could be pretty much regarded as equals without anyone able to exert any specific authority over the other). "I spoke to the captain while I was in there, and- between the parts where I was arrested and thrown into a cell as a spy- he mentioned something about the ship having discovered a weakness of some sort in Wraith technology that they were to deliver back to Atlantis; he appeared confident that it would turn the tide of the war. I admit that it's been several thousand years since they acquired that information, but given that everything we've found in the Ancient database suggests that the Wraith haven't really evolved that much since the original war with the Ancients, it's possible that it still applies to the Wraith in the present."

"..._Interesting_," Caldwell said, his tone reflecting his awareness that there was a catch to this news. "_You think you can convince the captain to give us the information_?"

"We have to try, anyway; I didn't come all this way for nothing," Sumner said resolutely (Another reason McKay could never get entirely comfortable with Sumner on a social level; he might not have been particularly keen on going to other worlds and into potential danger when he'd started, but the fascination of _seeing _those new worlds had generally replaced his initial concerns about what might happen to him out there, while Sumner still seemed to just regard this kind of thing as another 'business outing' without any real sense that he _enjoyed _what they were doing). "Doctor McKay, hook me back up to the pod; I'm going to try this again."

It was moments like this that left McKay frustrated; he went to all the effort to make sure Sumner could properly interface with this system- compensating for his slightly-below-average Ancient gene alone was difficult; the gene therapy had apparently only given Sumner the basic form of the gene, which meant he had some trouble interfacing with certain systems that even McKay could manage fairly easily-, but Sumner sometimes seemed to regard him as little more than a glorified technician who only found the answers because he was the team scientist rather than because he was at least one of the brightest minds on Earth (Calling himself the brightest mind in Atlantis wasn't as impressive given that there were only around a couple of hundred people in the city; there were less people for him to be smarter than in the city in that circumstance).

Staring in frustration at Sumner as he slid back into the pod, McKay stood up and walked over to another corridor, pulling up a nearby monitor screen to study the information on it without having to worry about keeping an eye on the colonel as well; it might be petty, but if Sumner wasn't going to show proper appreciation for his skills, he couldn't exactly be bothered keeping an eye on the guy twenty-four/seven in an environment that all evidence suggested wasn't going to be hostile anyway...

"_Doctor McKay_?" Caldwell's voice said after a few moments, breaking the silence that had settled over McKay as he studied the computer systems before him (The view of the virtual environment before him was actually rather fascinating, considering that it was based on nothing more than the impressions being transmitted into the minds of the users, despite the obvious similarities to the _Matrix _trilogy that was invoked by the idea of his 'translating' the code like this).

"Go ahead," McKay replied briefly.

"_Long range sensors have just detected two Wraith cruisers heading this way_," Caldwell replied grimly. "_No doubt coming to investigate why their scout ship was destroyed earlier_."

"What's their ETA?" McKay replied, his attention still engrossed in the information before him; the fact that the ships had just been picked up on long-range at least suggested that he wouldn't have to worry about the Wraith showing up here for a while now.

"_Little over an hour, and I plan on being long gone by then_," Caldwell applied grimly. "_What's the status there_?"

"I've been able to decipher some more of the program," McKay replied, grateful for a topic that took him away from thinking about the Sumner situation when he really couldn't be certain how he felt about that whole mess in the first place. "I'm actually reading the neural tracking signatures of the entire crew as they make their way through the-"

"_I meant Colonel Sumner's status_?" Caldwell cut in.

"Oh, him," McKay said, trying not to sound too put-out at the news that the expedition _still _seemed to lack a soldier in the upper echelons of the command structure who couldn't think of anything more than his next potential military acquisition as he glanced at his laptop. "He's still in the pod; no sign of activity yet."

"_Understood_," Caldwell responded. "_Just be aware of the time constraints; with the Wraith ships approaching, we can't risk being discovered_."

"Sure, right, ticking clock, I get that," McKay said, waving his hand impatiently despite the fact that the other man couldn't see it. "Anything else?"

"_If he's not out of there in thirty minutes, disconnect him manually_," Caldwell said simply.

"Right..." McKay said, only considering the implications of what he'd just heard when he'd terminated the radio connection.

It was another case where he wasn't sure what disturbed him more, really; the fact that Caldwell was willing to give an order to have someone manually disconnected from a system this complicated- although McKay had to acknowledge that there was a chance the _Daedalus _commander just didn't realise the implications of what could happen if McKay did what he'd suggested-, or the fact that he wasn't all that bothered about it himself.

It wasn't that he wanted Sumner _dead_, and he was confident enough in his abilities to get the man out manually if he had to, but he just found it slightly tragic that he was so willing to contemplate the possibility of attempting something potentially dangerous to someone who was meant to be on his team...

He'd never told this to anyone, of course- at the time he'd been too pig-headed to really register his thoughts and feelings on the issue, and later it had never seemed like the right time to bring it up-, but when he'd first met then-Major Carter during that incident with Teal'c being stuck in the Stargate, he'd actually been slightly jealous of her ability to form that kind of close relationship with somebody that she'd clearly shared with Teal'c- judging by the lengths she was willing to go to in order to get him out of the Stargate even after he'd insisted that it was hopeless (Although, looking back, the fact that she'd had practical experience with the gate as opposed to his second-hand- knowledge probably hadn't helped her believe in his 'statistics'); you didn't go to that much effort for someone you just worked with-; a part of him had slightly hoped that he'd form a similar connection with his teammates once he was on his own offworld team...

And here he was, giving genuine thought to attempting something that could leave Sumner with potential brain damage if he made a mistake?

It wasn't like he _wanted _to do something like that; he just couldn't shake the feeling that, if this had been SG-1 in this situation, Colonel Carter would be putting a lot more effort into trying to figure out a way of doing this without _any _risk of brain damage to the subject, while all he was doing was hoping that he wouldn't cause any if the situation came to that.

"_Doctor McKay_?" Teyla's voice said, breaking off his train of thought as she spoke over the radio. "_We have a problem_."

"Namely...?" McKay began, only be cut off mid-sentence by the brilliant gleam of an Asgard transporter...

* * *

Which subsequently faded to leave him standing back on board _Daedalus_, staring incredulously at Caldwell as the colonel sat in his chair on the _Daedalus _command deck, Teyla and Ronon standing on either side of him.

"What was all that about?" he asked incredulously. "I was still busy-"

"There is a Wraith on board the ship," Teyla explained.

Rodney's eyes widened in shock.

"_What_?" he said in horror. "But-but-"

"It's in one of those pods," Ronon explained, looking at McKay with a brief shrug. "Doesn't look like it's aware of us, and it seems to be the only one there, but-"

"Hold on; it's _in _a pod?" Rodney repeated, looking urgently at Ronon as he frantically tried to process what he'd just learned.

If a Wraith was _in _a pod, that meant that it was linked up to the virtual environment that Sumner was currently inhabiting.

Since there was no way that a Wraith could have survived on a shipful of Ancients in its natural appearance, that could only mean that it was in disguise somehow (To use a reference from _The Matrix_, it must have replaced its 'Residual Self-Image' with the image of one of the crew in order to blend in).

And, added in to what Sumner had mentioned about the Ancient crew working on upgrading their ship's hyperdrive...

"Oh no..." he whispered in shock.

"What?" Caldwell asked, looking pointedly at McKay.

"I need to go back there," the Canadian replied, deciding not to mention his theory until he had confirmation; he didn't want to suggest that something _that _bad was about to happen unless he was certain that it was about to happen.

"Out of the question," Caldwell countered. "With that Wraith in there, it's possible that the approaching ships already know about Colonel Sumner's presence in the network-"

"That is unlikely," Teyla put in. "We have already determined that the range of the Wraith psychic network is limited; the ships you informed us of earlier are presently too far away to make contact with the one on board the _Aurora_."

"Right..." Caldwell said, nodding briefly in a reflective manner before he turned back to McKay. "What would you actually be doing there?"

"Oh, nothing much; making sure that Colonel Sumner's all right in the environment, checking that the Wraith's access hasn't done anything to the system that I wasn't expecting, that kind of thing..." McKay said, shrugging uncertainly as he looked back at Caldwell. "I mean, I won't know what's there until I actually _look _at what's there, but it should be simple enough to find out how to deal with it..."

After staring at him in silence for a moment, Caldwell nodded in resolution.

"You've got fifteen minutes to figure it out, doctor," he said briefly.

"Fifteen _minutes_?" McKay repeated. "What _is _it with you military people and arbitrary numbers?"

"That's the time you have until I destroy the _Aurora _to stop the Wraith getting their hands on whatever's in there," Caldwell said in response.

"Ah," McKay said simply.

He had to admit, as much as he didn't like the time limit, he could definitely understand that reasoning for it; if this Wraith had encountered Sumner in there, the odds were good that it knew about Atlantis, which would _definitely _be a bad thing...

* * *

"So?" Ronon said a few minutes later as he and Teyla stood slightly further back from McKay, the scientist studying Sumner's brain patterns after analysis of the Wraith device connected to the pods had left McKay relatively satisfied that he knew what they were dealing with.

"Mmm?" McKay responded, glancing up at the Satedean before he remembered that he hadn't actually told them what he'd discovered in his analysis of the Wraith device. "Oh.... well, from what I saw of the Wraith equipment, they definitely found _Aurora _a long time ago- definitely long enough to have figured out how to access and reconfigure the system to accommodate their presence-, but barring some subtle traces of interference that looked like they'd just been installed when the Wraith actually accessed the system originally and were most likely the reason for the Ancients not remembering that they were in stasis in the first place, it doesn't _look _like they've done anything else to the system beyond allowing the Wraith in the network to look like somebody else."

"I... see," Teyla said, nodding slightly in understanding. "And... Colonel Sumner? Is he well?"

"Well, his brainwaves _look _fine, anyway; as far as I can tell, the only thing keeping him in there is the fact that he's probably still trying to find out what he can about that Wraith 'weakness' he mentioned earlier," McKay replied, shrugging slightly as he studied the readout on his computer screen. "No variation in his EEG frequencies, no sign of delta wave activity... as far as I can tell, there's nothing to stop us taking him out of here manually, although I _would _recommend a medical team on standby afterwards..."

"And what about that Wraith weakness?" Ronon asked. "Pretty sure that blowing this place up isn't a good way to find out what that's about..."

"Yeah, but I think we can safely say that if Sumner hasn't found it by now he's probably not going to get them to tell him it any time soon," McKay said, before he swallowed slightly as he looked at the other two. "Besides... I _think _I know what else they're up to."

"How?" Ronon asked.

"Well, I took a check through the ship's databanks while I was here- see what I could dig up, that kind of thing-, and-" McKay began.

"You accessed the ship's databanks?" Teyla interjected, looking uncertainly at McKay. "Would they not have the information we are looking for?"

"Normally, yes, but it looks like the Wraith erased the communiqué containing the information when it first gained access to the system; there's not even a password-protected file, never mind anything we _could _read," McKay said, shaking his head before he continued. "Anyway, that's not important now; what _is _important is that, according to Colonel Sumner, the Ancients in the simulation are working to update the _Aurora_'s hyperdrive to allow them to reach Atlantis faster-"

"So?" Ronon asked briefly.

"_So_," McKay continued as he turned to face the Satedan, "according to the Atlantis database, there are two kinds of hyperdrive; the basic interstellar kind, like the _Aurora _already has, or the _intergalactic_ kind, like the one that the Asgard gave us for the _Daedalus_. If my guess is right, with the information that Wraith's gaining from the simulation, he'll be able to learn how to modify the Wraith hyperdrives from inter_stellar_ to inter_galactic_..."

"...which will allow them to reach _Earth_..." Teyla finished, her eyes widening in horror at the implications of that deduction.

"All about their new feeding ground, huh?" Ronon said, looking grimly at the ship around them.

"Exactly," McKay confirmed, before he turned back to look at the still-immobile form of Colonel Sumner before them. "Which means that, right now, we _really _don't have the time to wait; we need to destroy this ship before those Wraith cruisers get here and the Wraith in the system can tell them what he's found out."

"Colonel Caldwell is already prepared to-" Teyla began.

"I found the self-destruct sequence while I was checking through the databanks; it'd be cutting it close, but I should be able to set it to go off a couple of minutes after we leave," McKay explained, turning his attention back to the data screen in his hands. "If I can just get Sumner out of the system..."

Before Teyla and Ronon could say anything more, McKay had hit a button on his computer screen and Sumner's pod had opened up, the colonel's eyes opening wide with shock as he stared at his surroundings.

"We're set!" McKay said, entering a few more quick commands into the console before him before he activated his radio. "_Daedalus_, we're set; get us to the medical bay!"

* * *

Looking back on the day's events that night in her room, the day's reports completed and the _Daedalus _on its way back to Earth, Elizabeth wondered if she'd ever been involved in a more tragic waste of a mission than this one had been.

They might have managed to destroy two Wraith cruisers and maintain the secrecy of Atlantis's continued survival- _Daedalus _had entered hyperspace just after the _Aurora_'sself-destruct had been activated, allowing them to confirm the cruisers' destruction without putting themselves at risk-, as well as gaining a brief but unique chance to get a look at an Ancient ship, but the fact remained that they had gained nothing of any kind of practical value from today's events, any chance to learn about the Wraith 'weakness' that the ship's captain had spoken about had been lost, and Colonel Sumner was still resting after being forcibly extracted from the stasis pod like that (He had apparently escaped suffering neurological damage, but according to McKay and Carson's assessment of his condition being forcibly extracted like that had essentially left his brain feeling like it had been sharply kicked and he would require at least a couple of days to recuperate).

It was almost unbelievably tragic, really; so many lives lost, with none of the Ancients even aware of what had killed them- according to McKay's reports they hadn't even known that they were in stasis in the first place thanks to the Wraith manipulation of the virtual interface-, and nothing gained from their sacrifice beyond the survival of people they'd never met...

Pushing her dejection aside, Elizabeth pulled a small bottle out of her cupboard, poured herself a glass of its contents, and raised it up in a one-sided toast.

"To the _Aurora_," she said simply.

It might have been toasting them for nothing, but she felt a need to at least acknowledge their existence.

They might have essentially 'died' long ago- as Ronon had commented during the debriefing, you couldn't call centuries spent trapped in stasis pods _living_-, but they had lived their own lives once; _somebody _had to acknowledge their passing...

It was like John, really; just because nobody else knew the full scale of what he had done for them- and not even she knew where he'd _come _from originally- didn't mean that he should go unmourned if he should die in the future...

Pushing those thoughts aside, Elizabeth swallowed her drink and then lay on the bed, lost in her thoughts of a now-destroyed Ancient ship and a strange man in a mask with a past that seemed as lost as the ship...

* * *

AN 3: Just to clarify, Sumner lacks Sheppard's ingenuity in the field, and hence never escaped his cell after he was locked up there because he never had John's idea of leaving and returning to the virtual environment to draw the guard in, and was thus never stunned during his escape and therefore left McKay with no reason to believe that the Wraith exerted a particularly significant influence over the virtual network


	11. We're All Mad in Our Own Way

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This chapter will look at some of the events that occurred during the two-part "Lost Boys" and "The Hive", but obviously reference to the precise details of those episodes will be limited due to the majority of the action taking place off-world where John, naturally, cannot go; it's not the most extensive rewrite, but I think it allows for some good insight into John's character at this point in his history

Mystery of the Phantom

As she stared out at the ocean before her, waiting impatiently for any sign of Atlantis's mysterious guardian to respond to her usual 'signal', Elizabeth wondered how wrong it was to be more concerned about the fact that she couldn't make contact with John than it was to be concerned about the now almost week-long absence of her military commander.

The more time she spent in this job, the more she began to appreciate how difficult it must have been for General Hammond back in the early days of the SGC; she might have lacked the general's practical experience at military matters, but she had at least entered Atlantis with relatively good- if primarily second-hand- knowledge of what kind of discoveries she might make out here in Pegasus, whereas Hammond would have been sending teams out into the galaxy with absolutely no idea about what he might be dealing with save for the knowledge of the Goa'uld's existence and their very real threat to life.

She just couldn't believe that things could have gone this wrong this quickly; the mission had seemed to be a perfectly straightforward assignment when it had originally come up. All they'd been doing was checking out a tip from one of Teyla's contacts about the location of a possible ZPM, and now Sumner and his entire team had been missing for several days with no sign of any kind of ransom demand or even a single unscheduled offworld activation that hadn't been immediately accounted for by a report from another offworld team, leaving them with no clue where the main team had gone and no idea what to do to find them.

Lorne and Zelenka were doing their best to run through some of the recently-dialled addresses from that planet's DHD, but given that they had no idea what order the addresses had been dialled in, it was still going to take ages to actually find what they were looking for, particularly since they had no guarantee that whoever had abducted Sumner's team would have stayed on the planet they went to after the original abduction; for all they knew the captors could have taken them to another planet afterwards...

"We have _got _to stop doing this," John said, his tone only slightly jocular as Elizabeth turned around to see him standing behind her in his usual relaxed manner. "Somebody's going to get suspicious at this rate; maybe I should set up a private phone-line..."

"Unlikely," Elizabeth replied, turning back to look at him with a brief smile. "Coming out here for air during a stressful situation is hardly _that _suspicious, and nobody ever comes out to bother me here anyway; it's a lot more straightforward than a giant floodlight in the sky, anyway."

"Quite," John said, smiling in a manner that gave no indication of whether he recognised the reference- he could have been smiling at the Bat-Signal reference or he could have just found the idea of attracting his attention in that manner unusual-, before he looked at her more seriously. "I can't do anything now."

"Oh," Elizabeth said, the smile fading from her face as she looked at him. "You're sure?"

"Positive," John replied with a solemn nod. "I'd like to help, believe me, but I've found nothing in the Ancient database that would allow you to carry out the current search at a quicker rate than what you're doing right now, and even if giving me access to the Stargate was possible, I can't contribute anything more than an extra pair of eyes to the current search effort."

"Good point," Elizabeth said, nodding briefly at him with a slightly sullen expression on her face, unable to stop herself expressing her slight dejection at the failure of this latest effort.

Then again, she supposed she should have expected this response from the beginning; she'd come here more out of habit than anything else. As John had made increasingly clear over these last few months since she'd returned from Earth, he could make mistakes and fail just as easily as any of them; there were times when even his evident skills couldn't make a difference to what they were dealing with...

"Well," she said at last, shrugging slightly as she indicated the door, the slight disappointment she felt pushed to the back of her mind once again, "I guess I'd better get back to work."

"Yep," John replied, smiling slightly back at her as he glanced upwards. "And I'd better get back to hiding."

Before Elizabeth could ask anything else, John had thrown what looked like a grappling cable from his belt towards a point above the balcony that she couldn't quite make out- she'd never been able to establish what all the various spires above them were for; they knew that some were transmitters and some were lightning-rods, but precisely which spires did what was still a mystery-, before pulling on the rope and sending himself flying upwards as though the line was on a reel of some kind, leaving Elizabeth staring up after him with a slightly stunned smile that swiftly faded into amusement.

"That's new," she said simply, forcing the smile from her face as she walked back into the control room; as amusing as it was to witness further evidence of the previously-perceived 'similarities' between John and Batman in the use of the grappling line he'd just demonstrated, if she walked in grinning when Sumner's team were still missing she'd attract far more attention than she wanted to.

* * *

After another couple of days with no progress, Elizabeth was increasingly finding herself contemplating drafting a letter to request official replacements for Colonel Sumner and Doctor McKay; Generals O'Neill and Landry might understand her reasons for continuing the search for Sumner and his missing team so far, but the IOA would only tolerate operations being suspended for so long before the expedition as a whole was ordered to resume their usual efforts to search for technology that they could use against the Wraith or the Ori...

The sound of the Stargate being dialled prompted her to get up from her seat and head for the control room, the shield dropping into place just as the seventh chevron of the incoming wormhole engaged.

"It's Doctor McKay's IDC," the technician at the Atlantis DHD said, looking back at her with a relieved smile that Elizabeth automatically returned.

"Lower the shield!" she said with a relieved grin, only half-noting the marines that were even now gathering around the Stargate; even if the new arrival turned out to be another Genii-esque attempt to take control of the city, at least they might have some information about what had happened to the missing team. For a moment, the sight of Doctor Rodney McKay walking through the Stargate brought a profound sense of relief to Elizabeth, and then she took in his appearance- wide eyes, constantly moving hands, a slightly silly grin on his face and perspiration lighting covering his skin as though he'd recently undergone some extreme effort of some sort-, and realised that the situation was still far from resolved.

"I know what I have to do!" McKay yelled as he walked through the gateroom, seemingly unaware or unconcerned about the guns around him (Elizabeth was better it was the first one; McKay would _never _be unconcerned about guns pointing at him).

"Rodney, what's happened?" she asked, looking urgently at the Canadian scientist, grabbing his arm before he could walk past her. "Where are the rest of them?"

"There's no time, no time," McKay said, his voice a rapid pace that Elizabeth had only heard him use in the past when he was feeling particularly frustrated or on-edge about something, pacing randomly around her as he waved his hands and breathed so rapidly that he was practically hyperventilating, his red-rimmed eyes doing little to console her. "The planet– not Ford's, the one the, uh, ship's headed towards-, we need to get there and we don't have much time; I was barely able to escape myself, but I managed to take out the guards."

He paused briefly at this point, but it was only to point at Elizabeth with a broad grin before he continued. "Oh, you should have _seen _me! I was amazing! I wish we'd got it on camera because... that's not the point!"

"Rodney," Elizabeth said, trying to control her immediate response- she had enough trouble right now without yelling at a man who was already clearly in a very difficult emotional state; she'd almost assume that he was high if it weren't for his overly-paranoid health concerns making it unlikely that he'd do this to himself-, "slow down. Are you all right?"

"Yes, yes," McKay replied, before he shrugged and let out a brief giggle (Elizabeth hadn't even known that McKay _could _giggle) before he began to pace again. "I mean, um... I dunno; I mean, I did take out the guards and they were huge and dumb and stupid and..."

"What guards?" Elizabeth asked, trying to sound more patient than she felt; McKay was hard enough to communicate with normally, but it was practically _impossible _with him in this condition...

"Ford's guards!" McKay replied, the brief moment of assertive insistence the closest thing to lucidity she'd seen him display since getting back. "Haven't I mentioned Ford?"

"No, you didn't," Elizabeth said, privately crossing her mental fingers at the reference to Ford; she was starting to get some ideas about what had happened to the rest of the team that she _strongly _hoped were the wrong ones. "And you haven't mentioned Sumner, Teyla and Ronon either."

"Yes!" McKay yelled, pointing triumphantly at her as though she'd just provided him with the missing piece of the puzzle that he'd been trying to solve. "They were there too, and there were the two guards; they were huge and massive and I had to take them out, so I had to inject some of the enzyme!"

"You _took some of the enzyme_?" Elizabeth repeated; she couldn't believe that someone as allegedly brilliant as McKay could have done something that _stupid_...

"No-no-no-no-no-no-no," McKay said, shaking his head as he continued to pace around her, his voice becoming increasingly high-pitched as he spoke, "I didn't take some of the enzyme. I took a _lot_ of the enzyme, because I _had_ to, because I had to take out the guards, which I did, and you should have seen me; I was _amazing_!"

"Are you insane?" Elizabeth hissed at him in frustration.

"Yes, yes," McKay replied, his face contorted slightly in pain as he spoke, evidently fighting to think his way through what he was saying. "Now that I've taken the enzyme, yes."

"Rodney, focus," Elizabeth said, grateful that at least the Canadian scientist had admitted to his current mental state; in her experience, if you were able to _admit _to being insane, you weren't so far gone that you couldn't be helped. "Where are the rest of your team?"

"No, no, no, I had to take the enzyme because... because I had to take out the guards!" McKay continued, talking as though he hadn't heard her before he began to pace again. "But that's not the point – the point is we don't have enough time; we need to stop the ship from getting to where the ship is going."

"OK..." Elizabeth said, placing an arm around McKay's shoulders in an attempt to guide him in the right direction. "Come on, let's take a walk to the infirmary, all right?"

"Whoa-whoa-whoa-whoa-whoa," McKay said, pulling free of her before they'd managed more than three steps. "What are you doing, where are we going? I don't wanna go to the infirmary, I wanna go to the, to the, uh..."

No sooner had McKay pointed at one of the side passages leading off from the gateroom than he collapsed to the floor, leaving the guards to hurry towards the scientist's fallen body.

"Doctor Beckett," Elizabeth said as she activated her radio, praying that what they were doing would suffice to help him, "we have an emergency; we're headed to you."

* * *

Sitting silently in the maintenance tunnel nearest to the infirmary, John could only listen to the low, weak and delirious rantings of the man that even the Elizabeth he'd originally met had called one of the most brilliant men alive- while making sure that he promised never to reveal _that _information to McKay if he ever found himself with the chance to tell his story to the expedition- and wonder at the sheer scale of what enzyme withdrawal could do to a person (Although he privately acknowledged that, based on what he'd heard Beckett say to Caldwell and Elizabeth earlier, this was probably the worst it would ever get, given that McKay was going cold turkey after taking a _really _large dose).

He'd known the stuff was dangerous, of course- the damage he'd caused to the rooms he'd locked himself in when he was 'detoxing' himself after particularly hard fights was proof enough of that; the door controls for a couple of the more distant rooms would probably _never _work properly after what he'd done to the control crystals before he'd stopped himself-, but his past experience with the stuff had been in relatively small doses on particularly desperate occasions, and even on his worst days he'd managed to burn through most of the enzyme fighting his way through the Wraith he'd been fighting at the time.

The sheer _scale _of what this stuff had done in larger amounts...

A part of him briefly wondered if it would have made any difference if he'd accepted Elizabeth's request/suggestion to help in the search- maybe he'd have been able to find McKay _before _the scientist had felt the need to do this to himself-, but he pushed that thought aside almost at once; he might be great at _using _Ancient technology, but he'd be the first to admit that sometimes the fine details of how some stuff worked wasn't his strong point, and hence there was nothing he could usefully contribute to the situation at this point.

And as for the possibility that the supply of Wraith enzyme he kept on him in case of emergencies could help McKay through his current state...

Given the minimal amount he possessed- enough for one, maybe two doses of slightly enhanced strength in a fight where he just needed an 'adrenaline rush' to push himself that but further; he always assumed when collecting the feeding sacks of the Wraith he'd killed that he just needed enough for the next fight and he'd 're-supply' then-, it wouldn't be enough; from what he'd seen and understood of Doctor Beckett's analysis, McKay had taken so much enzyme it had been practically a miracle he hadn't collapsed right away. The enzyme supplies he could offer were so minimal that they'd barely have given McKay any real relief, and would have essentially just made him take longer to come down rather than actually help him.

_Plus, of course_, the small, selfish part of himself that he hated to acknowledge the existence of reminded him, _you wouldn't want to damage your 'noble warrior/vigilante' image with the good doctor, would you...?_

As ashamed as John was to admit it, that part of him made a good point.

He might like to tell himself that he had also kept the existence of his enzyme 'stash' secret to stop Sumner becoming _more _'jumpy' about him- the man might be scaling back the search for him since the Siege, but John wasn't going to kid himself that Sumner was any happier about having a renegade element active in Atlantis than he'd been when he first learned the Phantom existed-, but the thought of Elizabeth's reaction to him was another problem; the thought of her looking at him like she'd looked at Ford... wondering if he'd use it and attack her while under the influence... doubting him because he resorted to drugs...

It scared him.

More than that; it _sickened _him almost as much as the thought of her learning about the people he'd killed during the Genii invasion had done (Although he had to admit that she'd never really confronted him about it, he always felt anxious when talking with her in case she chose to bring it up).

He might not be worthy of Elizabeth's love, but he'd earned her friendship; he couldn't bring himself to do anything that could jeopardise that...

At least, not unless he was _sure _that there was no other way to accomplish anything.

He dreaded the thought of what would happen when that day came...

"How is he?" the object of his thoughts said, prompting John to glance out of his tunnel and see Elizabeth talking gently to Doctor Beckett, McKay now sleeping peacefully in his bed; he'd been so caught up in his own thoughts that he'd missed the moment when McKay's already-weakened delirium had finally led him to sleep.

"Asleep, finally," Doctor Beckett commented. "Mercifully..."

"Has he mentioned anything about Sumner and the others?" Elizabeth asked, a brief smile on her face at the reminder of McKay's usual attitude before she looked thoughtfully at the scientist, her gaze the same kind compassion her older self had directed at him when he'd first arrived in this city...

"No, not yet," Beckett replied, a slightly wistful smile on his face at the memory. "Our conversation was of a different sort; I feel not unlike the priest in _The Exorcist_."

For a moment John wondered at the specific details behind that reference- he'd never actually managed to see that movie, even if he'd found what he'd heard about it intriguing-, but then Doctor Beckett turned the conversation back to McKay's condition. "Well, he's through the worst of it. The nausea has passed, his pulse has returned to normal, blood pressure in a more reasonable range, considering he was borderline hypertensia before taking the enzyme."

"Good," Elizabeth said briefly.

"I hate to say it," Beckett added with a rueful smile," but his stubbornness is probably what sustained him through the ordeal."

"Hmm..." Elizabeth said, raising her eyebrows before she looked back at the doctor. "We won't tell _him _that, though."

"Aye," Beckett replied with a slight smile. "Mustn't feed the beast."

"No," Elizabeth agreed with a smile before her eyes returned to the Scottish doctor with that same universal compassion that was one of the things that he had loved about her since the day he met her. "You should get some rest; you look exhausted.

"I'll stay with him just a wee bit longer," Beckett replied, his attention turning back to McKay. "Just to make sure he's out of the woods."

Even as Elizabeth turned to leave, John had already turned around to head for his usual resting-area in this part of Atlantis; with McKay clearly out of the woods and nothing to be done until he woke up to explain what had happened to the rest of the team, he might as well get some sleep...

* * *

The next morning, Elizabeth was, for once, primarily relieved to see Doctor McKay enter her office without a pre-existing meeting scheduled; most of the times he came by unannounced had resulted in her learning about some bad news that she could certainly have done without- if she hadn't listened to his overly paranoid concerns about Chaya they might have been able to learn more about her before she sealed her Stargate address off from them-, but right now anything he had to tell her about what had happened would definitely be appreciated.

"Good to see you back on your feet, Rodney," she said, smiling briefly at the scientist as she stood up and walked around her desk. "You gave us quite a scare there."

"Yes, it was very strange," McKay said, shrugging slightly as he contemplated his earlier behaviour. "The whole time I was under the influence of the enzyme, it felt like I was, uh, I was perfectly lucid– eloquent, even; that it was _you_ who wasn't making any sense or listening to reason. It was very peculiar. I think I kind of understand how Ford must have been feeling this whole time."

"Talking of Ford..." Elizabeth said, deciding that she might as well get straight to the current issue- if John had taught her anything in his time here it was the value of direct action in a crisis; diplomacy could wait for when there was more time to talk-, "what actually happened out there? And where are the others?"

"I don't know _exactly_, but I can probably figure it out," McKay said, heading for the main control room as Elizabeth followed him. "I told you Ford's alive?"

"It... came up," Elizabeth replied; it had been an unexpected bit of news, of course, but once again John had taught her not to take anything for granted no matter what you thought you knew. "What does he have to do with this?"

"He's been busy since we last saw him," McKay explained as he sat down at his station in the control room. "He gathered himself together a little gang, doped them all up on the enzyme. They're the ones that caught us, drugged us, and coerced Sumner, Teyla and Ronon to join them on a mission to destroy a hive ship."

"A _hive ship_?" Elizabeth repeated incredulously, leaning over to more directly address McKay.

"Yeah, they managed to steal themselves a Dart; like I said, he's been busy," McKay explained with a brief shrug. "Look, when they didn't return from the mission, I realised something had obviously gone wrong. Now, I have the coordinates to the planet that the hive ship was headed towards to cull."

"So, if the team's still alive- maybe captured on the ship-, there's a chance we can rescue them," Elizabeth concluded, hoping that her assessment of the situation was accurate; after the way things had been progressing on the search, any kind of information was a step in the right direction....

* * *

Later that day, the now-returned Sumner, Teyla and Ronon all resting in their quarters after their medical examination had concluded, Elizabeth was turning over Sumner's briefing in her mind, contemplating the new information that they'd discovered on this mission.

From what she'd gathered, Ford's plan to infiltrate the Hive by having Sumner pilot the Dart into it after 'culling' the rest of the team actually hadn't been that bad in principle- it might have been better with a more experienced pilot, but Sumner had taken a few basic flying lessons in the gateships recently and at least knew the essentials of what to do-, but the lack of resources on the part of Ford's team, combined with their limited knowledge about the fine details of the Dart's operating systems to begin with, had left Elizabeth feeling immediately sceptical about its chances. Even before she heard about how the Dart went into automatic pilot upon approaching the ship and two of Ford's team were lost before they were captured, it had been clear that Ford's use of the enzyme had reached a point where it was significantly impairing his judgement, and his later attitude on the hive-ship had only further reinforced that as he and Sumner apparently spent more time arguing with each other than they spent working on getting out of their cells.

In the end, they'd only managed to escape after the arrival of a second hive-ship at the planet where the culling was going to take place; after Teyla sensed their arrival, Sumner, using information Ford's men had gathered about division among the Wraith fleet- apparently the Wraith waking up so early meant that there was a 'food shortage' as the multitude of active Wraith found themselves at odds regarding how much they could cull now while still being sure of having a food source later-, had tricked the Queen of the Wraith hive by claiming that they were agents sent by the other hive to try and destroy the one they were on. When the Queen attempted to interrogate the rest of the team about Sumner's story, the still-crazed Ford, accompanied by the last of his team, had apparently attacked the Wraith soldiers, giving Sumner, Teyla and Ronon time to escape and find their weapons before departing the hive-ship in a dart, followed by Sumner using a trick that had been mentioned in an old SGC mission report- something about Apophis's first attempt to attack Earth directly, as Elizabeth recalled-, provoking the two hive-ships into attacking each other by firing on them in his dart before escaping to the nearest Stargate to return to Atlantis.

It wasn't the most organised mission ever, of course- three of her senior staff (Teyla and Ronon might not have any official ranks but she still regarded them as important parts of the command structure even if Sumner might argue the issue) had been temporarily technically addicted to drugs and Ford had almost certainly died when the Hive-ship exploded given that he was last seen fighting Wraith despite being heavily outnumbered-, but it had definitely turned up some useful information regarding the current social structure of the Wraith hives that they might be able to use at a later date...

_Ford_...

That was the real problem here, really.

Ford might not have been a member of the expedition for the last few months, but he'd still been someone she'd brought to Pegasus; the fact that he'd died because of a position that she'd contributed to him being in...

There might have been nothing that she could have done to save the young lieutenant from himself- finding one man in an entire galaxy was far from an easy task, after all-, but that didn't realistically make her feel any better about his loss, particularly when she still had to write the official letter back to his family on Earth...

* * *

As he sat silently in the small 'junction' that served as his sleeping area- a location where a few of the maintenance tunnels he used to travel around Atlantis intersected to create a larger space-, John Sheppard raised a glass of the closest thing to a bottle of alcohol he'd ever managed to acquire during his time in Pegasus; he hadn't exactly had much chance to drink before he'd come to Atlantis, but he kept a couple around to 'treat' himself on special occasions.

"To Lieutenant Aiden Ford," he said, wistfully tipping his glass in memory of the now-deceased lieutenant (Blowing up a ship when the guy was still on it definitely didn't _sound _like something he'd survive, after all). "May he rest in peace."

He might not have particularly liked Ford- the man had been far too 'by-the-book' for his liking; at that age he'd hoped that the younger man would have displayed more 'on-the-spot' initiative rather than just relying on Sumner's plans to get him through the situation-, but his heart had been in the right place at least.

Besides... the day he was _happy _about the death of a human...

He didn't want to know what he'd be like on that day, but he strongly hoped that it _never _came to pass.

He might kill humans when he had to- memories of the Genii invasion flashed through his mind-, but he would _never _kill anyone simply because he wanted to do so...

If he didn't maintain a line like that, how long would it be before he became the monster he was always afraid that Elizabeth would witness inside him....?

He couldn't help but shudder at the thought of that happening.

_Never_, he silently vowed to himself.

He'd seen what he could become if he didn't care during the Genii invasion, and his brutality had horrified him in the aftermath; he could _never _allow himself to become that monster again...

He just wished he could shake the feeling that there'd come a day when he would be unable to keep that promise...


	12. Questioned Epiphanies

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Not much happens in this chapter- it's essentially just my take on "Epiphany"-, but it does reveal what I think are some interesting hints about John's past and motivations...

Mystery of the Phantom

As he studied the landscape before him, Sumner had to admit that he was actually secretly enjoying this part of the current mission; even if it didn't result in any significant discoveries, it was a pleasant change to be able to get out and do some walking in an area where he _didn't _feel the need to run for his life, but could simply move around at a more leisurely pace. The vast mountain range before them was an impressive natural spectacle all on its own, while the glimpses he'd caught of the valley within the crater looked like a rather pleasant location to relax or take some walks on a day off (Even if natural defences like that were useless against an enemy capable of flight); even if it was still his reason for being there, the fact that McKay was interested in whatever object within the crater had caused that 'energy spike' that had prompted them to land the gateship in the first place was merely a pleasant bonus at this point.

He just wished that McKay would stop whining about how long it had taken them to reach this point; it wasn't like he hadn't _tried _to get them closer to the current path they were taking- the most direct route to the crater on the ground had been a partly-concealed path in a small stone canyon shielded from the casual view by trees and other assorted plants in the area; it would have taken a trained soldier to spot the area where the vegetation didn't quite line up with everything around it, and even then they'd need to actually know there was something here worth looking for-, but landing the gateships in an area this densely packed would have been difficult even for an experienced pilot, and he was still learning how to do more than the basic essentials of flight at this point...

"We're almost there," McKay said at last as they walked further along the canyon, studying the device he held in his hands; any attempts he might have made to complain earlier had been swiftly shot down by pointed glares from Sumner or Ronon (The man might have a rather ambiguous respect for the chain of command- to the extent that Sumner wasn't sure if Ronon was really loyal to them or simply going along with the expedition for the chance to kill Wraith-, but he could _definitely _make an intimidating impression), but nobody could fault him for speaking at this point. "Whatever we detected, it's definitely around here somewhere..."

"Any ideas what it looks like?" Ronon asked, glancing at McKay as he continued to study his surroundings, his hands around his gun in preparation for anything that might require him to use it.

"I'll know it when I see it..." McKay muttered briefly, before he turned to point to his left with a brief smile. "And I see it."

Walking over in the direction that McKay had just pointed at, Sumner pushed a few trailing vines away from the wall, revealing a small cave inside the cliff with a simple square archway carved through the wall.

"Looks like a door," Ronon said briefly, as the four of them walked into the cavern.

"Yes, it is," McKay commented, the sarcasm in his voice trailing off slightly as Sumner shot a brief glance over at him- professional conduct on missions was something that he expected and demanded from all of his team- before the team commander turned his attention back to the door before them. The door itself didn't appear to be much- the only thing that they could see on the other side was a stone cave that didn't appear to have anything significant in it-, but the presence of writing that Sumner clearly identified as Ancient to the right of the door more immediately drew his attention; it at least confirmed they were on the right track...

It was the words written _below _it that attracted his attention.

"What the _hell_...?" he muttered, walking over to stare at the words carved into the stone below the Ancient writing, only slightly aware of McKay having joined him as he studied the writing that should under no circumstances be here, with faint traces of moss growing slightly over them as though they'd been here for a few years- certainly long before the Expedition had arrived in Pegasus-;

**TIME DISPLACEMENT FIELD**

**DO NOT ENTER**

"Oh my God..." McKay whispered as he turned to look at Sumner, his eyes wide. "It's a time _displacement field_..."

"Which means?" Ronon asked, looking slightly uncertainly between the two.

"Basically, if this warning's accurate- and even if it's not I'd definitely prefer to get someone here to translate what the Ancient says before I even _think _about stepping through that door myself-, then time beyond that doorway is going at a _different _rate to what it's going at out here..." McKay explained, his gaze shifting between the door, the writing, and his scanner. "There's definitely _some _kind of energy barrier across the threshold, but there's no way to determine what it _does_, unless..."

He clicked his fingers in inspiration and turned to look at Teyla and Ronon, who were still looking between the two former Milky Way residents in confusion. "Get me a branch."

"What-?" Sumner asked, as McKay pulled a camera out of his pocket and smiled at him.

"You got tape?" he asked with a casual smile. "We tape this camera to the end of a branch- I didn't ask for a _log_," he said, changing tack mid-sentence as Ronon held out a large branch that looked more like a small tree, the Satedean subsequently stepping back to allow Teyla to step forward with a smaller branch while Sumner produced the previously-requested tape.

"Anyway, as I was saying," McKay continued, as he wound the tape around the camera as he held it at one end of the branch, "we extend the camera through, record for a few minutes, pull it back, and then play the recorder; at the very least, we'll be able to determine if there actually _is _a difference between the rate that time's flowing out here and in there."

"MALP on a stick," Ronon said briefly.

"Good description," Sumner responded, nodding at the Satedean with a brief smile.

"Yes, well..." McKay said, shooting a brief indignant glare at the two soldiers before he turned back to the door before them, extending the camera out just far enough to pass through the field, causing a faint blue glow at the point where it passed through the door like an object passing through water.

"I am not fluent in Ancient," Teyla commented from where she was studying the Ancient writing, "but I do recognise a few words; 'welcome' and 'ascension'."

"Ascension?" Ronon repeated.

"To a higher plane of existence," McKay clarified, rotating the 'MALP on a stick' to get a better view of everything on the other side of the field. "The race of people who built the Stargates eventually evolved to a point where they 'ascended' to a state of pure energy."

"That'd be great," Ronon comment with a slightly impressed tone to his voice.

"Yeah, well, sadly, it's a matter of, uh, evolution," McKay said, glancing briefly back at Ronon before returning his attention to the 'MALP on a stick'. "Anyway... I'm sure we've got more than enough now."

Pulling the branch out of the field, he casually turned the screen on and studied it, smiling slightly in confirmation. "Yep, it all adds up; the cave _looks_ perfectly normal, but the camera recorded over two hours of footage and the battery's nearly depleted after only a couple of minutes from this side..."

He shook his head slightly as he turned back to look at the writing on the wall. "What _doesn't _add up here is the warning..."

"You mean this writing in... English, correct?" Teyla asked, looking in slight confusion at McKay. "I understood that Ancient itself evolved into a language on your world; is it not possible that a similar language to the one you know could have developed independently?"

"Possible, but unlikely," McKay said with a firm shake of his head. "English evolved from a combination of so many different languages on our world, the odds of someone else developing the _exact same linguistic structure _for their written language a whole galaxy away from us are... are..."

"Really small?" Ronon finished for him.

"To say the least," McKay said with a brief nod before he turned his attention back to the writing. "Anyway, what we need right now is someone to translate the rest of this writing; maybe if we can find out _why _the Ancients set this place up in the first place we can get a better idea of what to do about it..."

* * *

"Fascinating..." Elizabeth said as she studied the writing before her- this was definitely one of the most interesting offworld translations she'd discovered since they came to Pegasus- before glancing back at the team that had requested her presence offworld; this was the first time she'd actually been called in to assist Sumner on anything other than the daily operation of the city- and even then he only took a peripheral position in all non-security-related matters-, and she had to admit that she was highly fascinated at the discovery. "And you're sure that time's flowing faster in there?"

"At a rate of two hundred and fifty to one," Teyla confirmed with a nod. "I sent my watch through while Colonel Sumner and Doctor McKay were requesting your presence."

"Good call," Elizabeth said, nodding in approval at Teyla while ignoring the slightly surprised look on McKay's face at the suggestion- berating him for a lack of respect for his colleagues wouldn't really accomplish anything- before she turned back to the translation that was her original reason for being here. "Anyway, I'm interpreting a bit, but it seems as though the field we're dealing with here was originally designed, not as a sanctuary from the Wraith, but a place the last of the Ancients could travel to and hopefully ascend without fear of attack."

"That makes sense," Sumner said, nodding in approval at the strategy. "They could spend lifetimes developing inside the field before any enemies even discovered that they were there in the first place."

"And anyone attacking the place would probably get ripped apart by the temporal stresses; quite frankly, I'm not sure if anything _we've _got could cope with what we'd deal with if we tried to get through that force field," McKay put in.

"What does the writing actually say?" Teyla asked, turning the group's attention back to the central issue.

"Well, based on this, the writing serves as a welcome and a warning for any humans who come here under the Ancients' protection looking for sanctuary," Elizabeth explained. "Judging from what I can understand here, I think it was left intact for anyone who came here to use it to seek the path to Ascension on their own..."

"And what's the warning?" Ronon asked, with his usual direct manner.

"That once you cross the threshold, there's no return," Elizabeth answered.

Personally, she found that part of the field's design a bit extreme- surely Ascension should be about making a _choice_, and it wasn't exactly a choice if you began to breed inside this field and never got the opportunity to leave it if you disagreed with how things worked-, but it had all been designed so long ago that there wasn't much point dwelling on it; the situation was what it was, and nothing was going to change it.

"Ah," McKay said, nodding slightly in understanding. "Well, that _would _explain why someone left the 'Do Not Enter' sign there, even if that doesn't explain why they wrote it in a language that _nobody _on this side of the galaxy could know..."

"Yes, it's... very strange..." Elizabeth reflected, even as she couldn't help turning over the implications of the message in her mind.

It might only be a theory, but she couldn't ignore the fact that there was at least one person in this galaxy who had a distinctly English-sounding name that nobody else knew about, who could _very _easily have been to this planet...

"So, as long as we're here, maybe we should... take a look?" McKay said, indicating the door with an uncertain shrug. "I mean, something this big _has _to be powered by a ZedPM; if we can get in there and shut it off-"

"No," Elizabeth said, shaking her head as she looked back at McKay.

"Pardon?" McKay said.

"Putting aside the fact that we can't even know for certain if you'd even be _capable _of extracting the ZPM- if there even _is _a ZPM there; for all we know this field could be generated by drawing on energy from the planet's core or something like that- from whatever device is responsible for generating the field, I'm not entirely comfortable with the idea of shutting down something that could be protecting an entire civilisation from the Wraith if someone's inside there, particularly given our inability to communicate with anyone inside the field." Elizabeth asked with a slightly pointed stare. "And besides, I admit that... temporal mechanics... like this aren't my strong point, but if time suddenly starts flowing at a different rate for you while you're inside the field that you're turning off, I'm not _entirely _sure that what would happen to you would be beneficial...."

After a moment of silent staring between the two, McKay nodded slightly.

"Point," he said, groaning in frustration as he stared at the cave before him. "So... all this way for nothing..."

_Nothing but more questions, anyway_, Elizabeth reflected to herself, silently studying the writing written underneath the Ancient text.

Even if John _had _written that warning... how could he have learnt how to write in English all the way out in Pegasus?

* * *

Staring at Elizabeth as she stood on 'their' balcony that night, a part of John tried to encourage the rest of him to do what he'd always done and go to her even as the rest of him knew that he couldn't do it without attracting too many questions.

He knew that it had been a dangerous thing to do when he carved those words into the wall below the Ancient writing- and it had taken a _ridiculously _long time to find a decently-sized chisel to do that job; that rock was _really _solid-, but he couldn't _not _do anything; the possibility of someone else getting stuck in there like he'd been trapped himself wasn't exactly a pleasant one, particularly when the odds were far slimmer that there'd be another Ascension-seeking civilisation inside the field who'd Ascend while the new guy was there and subsequently be able to 'negate' the time dilation field long enough for whoever it was to get out...

It had been an interesting time in its way, he wasn't denying that- the meditation techniques he'd learnt while he was living among them had definitely helped him maintain his focus while he was 'detoxing' himself after needing to use the Wraith enzyme on his missions, and that woman (Alyra, her name was) had been the closest thing he'd really had to a friend since the elder Elizabeth had died-, but it had never really been a _home _for him; even in those long-ago days, 'home' for him had already become Atlantis, and he'd been constantly eager to get back there before Elizabeth and the expedition had come through...

Still, no matter how defining a role his time there had played in his development, John just wasn't ready to answer the questions Elizabeth would obviously want to ask him regarding his knowledge of English and where he'd learned it; that would just lead into questions of how he'd come to be here and why he'd stayed here for so long that he just...

He wasn't _ready _for them, he supposed.

He knew that it was irrational to be afraid of how she'd react if she knew the truth about him, of course- the elder Elizabeth had been nothing but kind to him during the brief time they'd spent together-, but it was one thing to give helpful information to a scared fifteen-year-old boy in that state and another to accept a war-hardened man in his mid-to-late thirties (That time in the time dilation field had _really _thrown him off regarding how old he should consider himself now) in the same state; there was no guarantee she'd be anything like as accepting of him as her previous self had been after what she'd seen him do...

In the end, it wasn't worth the risk; better to avoid Elizabeth until the incident had been forgotten about in the midst of the next situation that required the two of them to talk about things.

He might have to tell her everything _eventually_, but he would tell her the truth about himself when _he _was ready to do so, not when circumstances forced him into a position where it seemed like he had to do so...

If nothing else, he never liked the idea of being 'forced' into something by accident; even his self-imposed 'exile' to Atlantis- while it hadn't been his choice to come to the city- had only lasted this long because of his decision not to go back after he'd learned what he was dealing with...

_Sorry, Elizabeth_, he thought, glancing in the direction of the balcony where the woman he would always love waited for a visit that, for the first time in the past year or so since they'd started that particular 'habit', would never take place, _but this isn't the time for me to tell you what you want to know_.

* * *

AN 2: Well, hope you all enjoyed that; next chapter features further Kavanagh-bashing as John comes face-to-face with his first Goa'uld during the events of "Critical Mass"...


	13. Can You Hear the Bomb Tick?

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Mystery of the Phantom

Sitting silently in his usual observation point above the main control room, John couldn't help but allow himself a brief hope that their current almost month-long record of time elapsing without encountering some kind of danger to Atlantis was about to be broken. The only currently-scheduled offworld mission was Doctor Zelenka's trip to check on the EM field on MGM-767- a mission that was pretty much guaranteed to be the proverbial cakewalk given the Wraiths' inability to land here (Where had that expression come from anyway... and he _really _needed to stop letting his mind wander at moments like this) even if he wasn't that happy about it-, the recent scans of a couple of passing Wraith cruisers firing at each other suggested that the recent Wraith civil war Sumner's team had learned about from Ford's men was still going on to great effect, Teyla and Beckett were heading off to the mainland to check on an old Athosian woman- he vaguely thought he remembered who they were talking about, but he wouldn't like to swear to it; keeping track of names wasn't exactly easy-, and McKay was still feeling uncomfortable about Cadman ever since she'd spent that time stuck in his head a few months ago...

Quite frankly, the most interesting thing that seemed set to happen today was the current dial-up to Earth to update them on their latest progress, and even that was relatively uneventful; so far nothing overly interesting had been discovered in Atlantis that they hadn't known about already...

Then John heard McKay yelling at them to stop dialling before they had input the last two chevrons, and he instantly re-evaluated his earlier assessment; it sounded like things were just about to get a _bit _more interesting...

* * *

Even as she walked into her office after hearing the latest news, Elizabeth almost couldn't believe it.

The Trust had planted a _bomb _in _Atlantis_?

She'd known that the renegade NID organisation had become the most powerful Goa'uld based organisation in existence following the fall of the System Lords last year, but the idea that they'd acquired enough influence to get an agent all the way out here in Atlantis...

That terrified her almost more than the thought of how close they'd all come to being destroyed did; threats to her life were something that she'd almost grown used to, but the scale of the Goa'uld's reach was a _definite _point of concern...

"We need to disconnect the ZedPMs and switch to back-up naquadah generators to prevent any possible dialling of the gate to Earth," McKay said, the immediately-available senior staff of Atlantis now gathered in her office to discuss what action they should take next.

"I agree," Elizabeth confirmed with a brief nod. "In fact, as of this moment, all 'gate activity should be suspended; how many offworld teams do we have out there?"

"Zelenka's team on M7G-677 is pretty much it, and they can safely be left where they are for the moment; it's not like the Wraith can get there anyway, and the natives are friendly enough," Sumner said briefly; he'd never been a particular fan of the inhabitants of M7G-677 when he'd been there, unable to bring himself to comprehend their 'suicide pact' even after McKay learned of the alternate explanation for why the founders had imposed that 'rule' in the first place. "I assume the _Daedalus _is still in range to relay a data transmission back to the SGC?"

"Yes, they're, uh, holding a position that keeps them in range of both Earth and us," McKay responded.

"Good," Sumner said with a brief nod. "Let them know that we received their message and aborted the dialling, and see if they can tell us more than 'there's a bomb in Atlantis'."

"The Trust probably think this is the only way to make sure that the Wraith don't back to their galaxy," Elizabeth put in, drawing the focus of the discussion back to the more central issue of the bomb's origins rather than their current lack of information about it.

"Well, it's drastic, but effective," McKay admitted with a brief nod.

"What's worse," Elizabeth continued, looking around at the others to ensure they understood what she was about to tell them, "is that the Trust operative who planted the bomb probably did so under orders from the Goa'uld."

"_What_?" McKay yelled, looking in shock at Elizabeth.

"Yeah, I remember that file," Sumner said, nodding in understanding at Elizabeth before he looked over at McKay. "The Goa'uld infiltrated the upper leadership of the Trust several months ago, giving them a stronghold on Earth and access to various government agencies; with the System Lords having been virtually wiped out, it's probably the most powerful Goa'uld-based organisation left in existence."

"What's a Goa'uld?" Ronon asked (Elizabeth couldn't help but feel somewhat frustrated at herself after that last statement; Ronon had spent so much time working with them and yet they'd failed to tell him virtually anything about the enemies they'd faced back home).

"Essentially," Sumner said as he looked over at the Satedean, "a Goa'uld is an alien snake that can enter peoples' heads and take control of their bodies; they ruled a substantial portion of our galaxy in the past by posing as gods."

"They don't sound pleasant," Ronon said in what was probably a reflective manner for him.

"Trust me, they're not," Sumner said briefly, his grim tone a reflection of his prior contact with the Goa'uld during his time affiliated with the SGC prior to his arrival in Atlantis as he turned to Elizabeth. "I'll organise teams to examine the most likely sabotage locations where a bomb might be stored."

"I'll check primary and secondary systems for any anomalous energy readings that might indicate the presence of an explosive device," McKay added.

"And I'll do what I can to contribute," a voice said from the door, prompting the group to turn around to see the Phantom standing at the door, his arms folded under his cloak and the technicians in the control room all looking uncomfortably at the man in the mask as though uncertain whether they should have done something to stop the Phantom reaching the office.

"Phantom?" Sumner said, glaring slightly at the figure in the door. "What are you doing here?"

"As I said, I'm here to help; nobody knows the fine details of Atlantis's construction like I do," the Phantom replied (Elizabeth noted that he was taking care not to look at her, but made a mental note not to be upset at this decision; it wasn't like he _could _show too much attention to her without risking giving away their secret contact with each other). "Add in the fact that you can guarantee that I'm _not _an agent of the Trust, and I think that it's fair to say that you can't exactly ignore my help."

After a moment's brief silence as he stared at the Phantom, Sumner nodded.

"Point," he said simply. "I'll assume that, in exchange for your assistance, you want confirmation that we won't attempt anything... untoward?"

"Precisely," the Phantom nodded. "Add in the fact that I can assure you I'll provide you with something useful at the conclusion of this particular affair if you let me handle this my way, and..."

He shrugged. "Trust me; it's in your best interest to give me relatively free reign in tackling this situation."

"Agreed," Elizabeth confirmed, allowing herself a brief smile at her... friend, she supposed would have to be the best term... as he walked into the office. "Do you have any-?"

"You're the Phantom?" Ronon said, his gaze giving no indication how he felt about this meeting.

"I am," the Phantom replied, nodding briefly back at Ronon. "And you're... from Satedea, correct?"

Ronon didn't answer verbally. Instead, he stood up, walked over to stand in front of the Phantom, and launched a single punch at his face, the resulting clang of metal being struck making it clear that Ronon had hit the Phantom's mask with exceptional force even if the subsequent appearance as the Phantom regained his balance after the punch gave no indication that his mask had been damaged in any way.

"Let me guess... for not being there for Sateda?" the Phantom asked, his stance giving away just as little about his feelings on the matter as Ronon's own.

"Pretty much," Ronon replied. "Probably couldn't have done anything if you _were _there, I admit, but it's the principle of it."

"I understand," the Phantom responded with a brief, accepting nod. "Just so long as you believe me when I say that I would have done whatever I could to be there when the attack came if I'd known about it..."

"I get that," Ronon nodded. "Big galaxy; you can't be there all the time."

"Thanks," the Phantom said, before he turned to look at the others, both men clearly having said all that they wanted to say at this time. "OK; what have we got so far?"

"Well, Lieutenant Cadman's going to be assigned to the search- she's one of the best bomb experts we've got-, but that aside all we can do right now is track this bomb down and take it from there," Sumner said simply. "Once we know where the bomb's been planted, we can work out _who _planted it from that point onwards."

"Good strategy," the Phantom said, as he walked around Elizabeth's desk to indicate the computer. "If I may; I've got a better idea of where a bomb _hasn't _been planted at this point than you do."

"Go ahead," Elizabeth said, nodding briefly at him as he sat down and pulled up a map of Atlantis before she turned to the others. "We'd better ask Colonel Caldwell to return here to assist in the investigation."

"What?" Sumner said, looking at her. "We'll be cut off from Earth if _Daedalus _comes back here-"

"True, but it's also the best way to question whoever on board that ship may have been responsible for planting the bomb here in the first place," the Phantom said as his fingers continued to tap away at the keyboard with a casual familiarity that nobody present was sure what to make of.

"Precisely," Elizabeth confirmed, before she looked around at the others. "Alright, let's get moving; we have a bomb to shut down."

* * *

With both of the city's ZPMs now disconnected from Atlantis- the original ZPM might have been down to around a tenth of its original power at best but even that was enough to trigger a decently-sized explosion if it was triggered under these circumstances-, the search progressed relatively swiftly, particularly with the Phantom's 'inside information' able to eliminate certain parts of the city from the search effort such as the pier power distribution sensors (Sumner made a mental note to ask the Phantom _how _he knew about those areas once this was over, even if he doubted that the Phantom would give up that information as part of his 'agreement' with them; he was only just willing to believe that the Phantom was willing to help them keep the city intact after the effort he'd put into defending it until he received incontrovertible proof of the Phantom's true agenda). The latest news relayed from Earth via the _Daedalus _was able to confirm that the 'trigger' that would detonate the bomb had been planted on Atlantis rather than back on Earth, which at least gave them a slightly better idea of what to look for, but that didn't help matters when they still didn't know where to look.

"_Nothing on the grounding stations_," Sumner said over the radio as his team completed their survey.

"Understood," Elizabeth said, nodding into her radio at the latest report as she glanced over at where McKay and Cadman were going over the internal sensor readings with the Phantom (Cadman and McKay might be able to identify unusual energy signatures, but the Phantom would have a better idea if the signals were meant to be there in the first place). "Be advised; we just received a second message-"

"_DHD_!" the Phantom- she couldn't think of him as John; the possibility of a mistake was too great- suddenly yelled, dashing over to the dialling device just as it began to dial what even at Elizabeth's current distance looked like Earth's address, only for the Stargate to shut down before it could complete the program.

"_Hah_!" McKay said, grinning as he joined the Phantom in looking at the DHD before glancing back at Elizabeth. "Good thing I pulled the ZedPM; whoever planted the bomb must have devised a programme that would upload itself and automatically dial the gate if the first dialling was halted-"

"As well as transmitting a distress beacon?" the Phantom said, glancing over McKay's shoulder at the screen on the wall, showing a dot on one of Atlantis's piers emitting a signal of some sort.

"Oh, _no_...!" McKay groaned, staring at the screen in frustration. "The 'gate dialling itself was just a means of drawing our attention away from _this_-!"

"Not any more," the Phantom cut in, walking over to one of the Ancient consoles and tapping a couple of buttons, shutting the system down with what almost looked like a flourish as he turned back to the others. "Sorted."

"Not quite..." McKay muttered, walking over to study the long-range sensor screen with evident apprehension before looking back at the rest of the staff. "The damage is already done; those two Wraith cruisers we detected earlier have altered course and are heading straight for Atlantis.

"_Damnit_..." the Phantom muttered, looking upwards in frustration. "No _wonder _we're not finding anything..."

"Pardon?" McKay said, looking at the Phantom inquiringly. "What's that meant to mean?"

"Come on, look at the facts here; the person who planted the bomb diverts our attention so that the _distress beacon _can be activated at a moment when a couple of _Wraith _ships are going to be able to pick it up?" the Phantom said as he stared pointedly at McKay. "What does their approach mean we'll have to do?"

"Uh... cloak the city?" Chuck the technician put in, looking slightly uncertainly at the Phantom (The junior staff were still evidently uncomfortable with the Phantom's presence in the control room; even if he was helping them, the man made for an imposing figure).

"Bingo," the Phantom confirmed, nodding briefly at Chuck before turning back to McKay. "And _what _do activating the city's cloak and dialling an inter-galactic wormhole have in common?"

"They both need the ZedPM to work-" McKay began, looking at the Phantom with an expression that suggested he was having to explain to someone how to use two and two to make four.

"Exactly," the Phantom said with a nod. "Blowing up a couple of Wraith ships wouldn't make any real impact on the Wraith fleet as a whole- even with the numbers they lost in the recent siege there's still around fifty hive-ships out there, and these aren't even _hives_, they're just cruisers-, but what if our bomber wants to put us in a position where we _have _to use the _ZPM_?"

"Of _course_..." Cadman said, her eyes widening in understanding as she turned to McKay. "You've always emphasised the explosive power of the ZPMs; if one of _them _exploded-"

"And if someone shut down the failsafes that _stop _it from exploding in the first place by leaving us unable to control the amount of power we're drawing from it at any one time..." McKay continued, horror dominating his face as he thought about the implications. "Oh my God..."

"Precisely," the Phantom said grimly, nodding at McKay as he indicated the nearest laptop. "Well, best get down to business then, right?"

"What do- oh, reactive the failsafes," McKay said, nodding in understanding as he sat down at the screen and began to tap rapidly at the laptop, pulling up the relevant systems and cursing after a few minutes' analysis of the code. "Ah, _crap_..."

"What?" Elizabeth asked uncertainly.

"Evidently, whoever set this whole thing up isn't as _idiotic _as we are," McKay said, staring in frustration up at the Phantom. "Whoever was responsible for shutting down the failsafes not only set it up in such a manner that the city's sensors didn't detect it, but also added in a code to block access to the systems necessary to reactivate them."

"OK," Elizabeth said, nodding slightly at her head scientist. "With that in mind, our first priority should be to disable the DHD- it's the quickest means of drawing power from the ZPM-, and then get on with turning those failsafes back on."

"I'll get right onto that," McKay said, getting up from his seat and walking over to the DHD, before he paused and looked back at Elizabeth with an uncertain stare. "Unfortunately, any number of systems can be used in conjunction with each other to, uh, overload the ZedPM; it'd be a much more gradual build-up than dialling the Gate, which would cause an instantaneous power spike, but, um, equally as effective in its results."

"And we still need that ZPM to activate the cloak when the cruisers get here..." Elizabeth groaned, nodding in understanding of McKay's point.

"On the bright side, dealing with the Wraith once we've got the cloak up is simple enough," the Phantom added, smiling slightly over at Elizabeth, even as the grimness of his gaze made it clear that he recognised the continued problem of getting the cloak up in the first place. "If you take a transmitter and dump it- along with some charred rubble- on a beach on the mainland, they'll probably assume it's just jetsam that washed up when the city exploded during the siege."

The smile faded as he turned his attention back to the code in front of him. "The problem now is working out who among our suspects had the technological know-how to add something like this into systems _I _don't even understand..."

"Hold on; you _don't _understand these systems?" Chuck asked, looking at the Phantom in surprise before McKay could voice his own thoughts on that topic. "But you've lived here for _decades_-"

"I know enough to get by; that's not the same as knowing enough to _change _things," the Phantom explained. "I've got a good working knowledge of _how _Atlantis works, but don't ask me to change any of the fine details of its operating system; that's a _bit _beyond my abilities..."

Looking at the masked man who'd helped to save the city so many times, Elizabeth wondered what it was about that statement that made her feel uncomfortable; he was being remarkably _casual _with people he'd only just met-

Then it hit her.

The Phantom was lying.

He wasn't lying _completely_- he was definitely telling the truth about the fact that he didn't know much about how to change Atlantis's programming code; she hadn't become a diplomat by being easy to lie to-, but she doubted he was as ignorant of it as he claimed he was...

Still, it wasn't her concern; anything that helped John remain safe without compromising Atlantis was fine with her (And when had she reached the point where those two were almost of _equal _importance to her?)...

Shaking her head to push those thoughts aside, Elizabeth turned her attention back to the matter at hand; with McKay having confirmed John's theory about what the Trust spy had done to set Atlantis up to explode, that left them with only a relatively small suspect list to choose from, and right now- if her memory served her correctly-, the man who'd have to be her prime suspect for this whole mess was currently on board _Daedalus_...

_So much for maintaining contact with Earth_, she thought, as she turned around to look at the technician currently monitoring Atlantis's long-range communications systems to keep them in touch with _Daedalus_.

If her current theory about the person responsible for this latest threat to her city was correct, not only would they _have _to abandon any thought of regular contact with Earth to directly question their suspects, she was about to have to deal with some issues regarding the methods used to get the information they needed that she was _not _looking forward to confronting...


	14. The Enemy Within

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Some medical details here regarding dislocated limbs that I'm not that sure about- along with a couple of general details about the chapter as a whole that I'm a bit ambiguous about-, but it was the best thing I could think of for the events depicted that wouldn't cause any serious long-term damage so long as the person responsible knew what they were doing

Mystery of the Phantom

A couple of hours later, _Daedalus _now in orbit of Atlantis and the passenger manifest having been transferred down to them to check for any inconsistencies- the possibility that someone had sneaked on board _Daedalus _after planting the program in Atlantis's systems to escape being caught in the explosion at this end couldn't exactly be overlooked-, Elizabeth found herself sitting silently in her office as she studied the personnel files before her, wishing that she could avoid this duty.

She might be used to suspecting people of having ulterior motives when she was drawing up treaties in the past- making sure that everyone got something out of the treaty without appearing to favour one side over another was never easy-, but that was when dealing with people that she didn't know personally; when faced with the possibility of suspecting someone that she knew- and most likely someone that she had _appointed _to a position in the first place-, it was far more difficult to be objectively rational...

"Problem?" a voice asked.

Glancing up, Elizabeth couldn't stop a slight smile at the sight of John standing in the door of her office, looking at her with the slight concern that was all she could realistically expect from him in the current circumstances (Sumner accepting his aid during this crisis was one thing, but the knowledge that Elizabeth had made prior contact with the Phantom probably wouldn't go down very well). There might have been a guard standing just at the end of the corridor with his gun not-quite-aimed at the Phantom in the event that he tried anything, but somehow, Elizabeth couldn't shake the feeling that it felt... _right_... for John to be able to drop in on her like that, rather than their secret meetings on her balcony...

"Just the obvious," she replied, pushing those thoughts to the back of her mind as she looked back at him. "Having to suspect one of our own..."

For a moment John's mouth seemed to twitch in a slight smile as he looked at her- it was only when she realised that she'd just referred to the Atlantis personnel as 'our' own as though she and _John _were the heads of the Atlantis expedition rather than her and Sumner; the fact that John was slightly pleased about that inspired something that even she wasn't sure how she felt about it-, but then the smile faded as he looked at her.

"If it's any consolation," he said, his voice slightly lower as he walked towards her- evidently he didn't want the rest of Atlantis's staff to know just how much he knew about them; Elizabeth still wasn't entirely sure how to feel about the fact that he trusted _her _more than he trusted the rest of her staff-, "I _do _have one obvious candidate you might want to question first, _and _I have a few small ideas about how to get more out of him if he proves initially uncooperative..."

* * *

"You think _I _did it?" Doctor Kavanagh said, looking in evident frustration at Elizabeth; clearly his transfer back to Earth had done little to improve on his original attitude to life on Atlantis.

"Relax, doctor," Elizabeth said, walking around the small table they'd set up in one of the conference rooms to enable a more direct interrogation of their suspects. Getting Caldwell to agree to these interviews being conducted on Atlantis hadn't been easy, particularly when he'd insisted on questioning those on board his ship before she did, but Elizabeth and Sumner had convinced him to leave it alone by pointing out that the investigation fell under Atlantis jurisdiction and they were therefore the ones who would be responsible for the interview. "You're just one of many people I'm questioning-"

"No, I'm pretty sure that mine's the first on what is probably a very short list," Kavanagh countered, his eyes flicking briefly over to the marine standing guard at the room's door before turning back to glare at Elizabeth.

"Shortly after the siege, you couldn't wait to leave Atlantis," Elizabeth elaborated (She couldn't allow herself to think about what Kavanagh had just said; the fact that he was accurate about being only one of a few suspects didn't mean it was something she liked to consider in depth). "A few months later, I received an urgent request from you to be allowed to return. Your second tour lasted three weeks, and suddenly you asked to leave again-"

"Yeah, because working conditions were intolerable for me here," Kavanagh interjected. "I have _no _friends here, my work is not respected-"

"And this occurs only days before we discover that someone with _excellent _computer skills has managed to rewrite Atlantis's operating systems and disable the failsafes that prevent the ZPM from overloading," Elizabeth countered herself, leaning forward slightly as she continued to stare coldly at him. "Add in the fact that you were _very _eager to leave the city before it happened-"

"Oh, so _obviously _I did it!" Kavanagh spat in frustration, sitting back and folding his arms as he glared scathingly at her.

"Given the circumstances, I'm sure that you can see how that behaviour could arouse suspicion?" Elizabeth countered, trying to sound reasonable despite her growing frustration with the man before her.

"_Your _suspicion, sure," Kavanagh retaliated. "Seeing as how you never cared for me, nor valued the talents I brought to this expedition."

"My personal feelings towards you, no matter what they may be, have nothing to do with this," Elizabeth replied, even as she made a mental note to actually look up whether Kavanagh had actually contributed anything to their time here that she should know about; as much as she disliked him, it _was _possible that she might have ignored his better work because of her personal prejudice against him rather than because it hadn't been that good...

"Oh, _please_!" Kavanagh spat, dashing any thoughts of sympathising with him out of Elizabeth's mind. "Everything you _do _is motivated by personal feelings. You're driven by emotion, not reason! It's why I've always felt you're not capable of doing this job; you don't have the-"

Noting the glares he was starting to receive from Elizabeth and the marine at the door, Kavanagh stopped himself finishing with the word he'd been originally planning to use and amended his choice to, "...strength... to be leading the fight against the Wraith."

"If I remember correctly, you were the one who wanted to- what was it?- run and hide?" Elizabeth asked, her arms folded as she glared critically at the man before her.

"And at the time, I was right; if the _Daedalus _hadn't arrived at the eleventh hour, this city and everyone in it would have been wiped out because of your recklessness," Kavanagh countered with a scornful snort. "There's no need for The Trust to blow it up when Doctor Weir's at the helm!"

Elizabeth stopped herself from making her desired automatic response that the expedition had actually been doing rather well even before the _Daedalus _arrived thanks to the assistance of the Phantom...

And that was even _before _she factored in Kavanagh's own lack of contribution to the siege; from what she recalled of McKay's staff evaluations of his team's performance during the siege, Kavanagh had been rather uncomfortable with their reliance on the Phantom, spending most of the time working on his own separate computer while everyone else focused on a group effort involving working out the timing of the bombs or how to extend the punishment the shield could take...

"Seeing as how this isn't getting us anywhere," Elizabeth said, standing up and glaring pointedly at Kavanagh, "I'm going to let someone _else _take over here."

"Oh God; you're doing 'Good Cop, Bad Cop' now?" Kavanagh groaned as he stared after her as she walked to the door of the conference room. "You can't be serious-"

As Elizabeth closed the door behind her, cutting off all but the loudest sounds within the room from the outside world, she could only hope that her faith in John wasn't misplaced; if he actually went as far as he'd gone when fighting the Genii- that secret, shameful part of herself couldn't stop her from remembering the condition that some of the bodies had been in when they'd been discovered, faith in John momentarily outweighed by the memory of the brutality of what he'd done-, then the chances of Sumner or anyone at the SGC accepting him taking a larger role in the city were virtually nonexistent...

* * *

Further thoughts from Kavanagh were cut off as the door to the conference room closed, followed almost immediately by someone grabbing Kavanagh's arm and pulling it rapidly backwards with a clearly audible 'pop', Kavanagh only just opening his mouth to scream before a gloved hand was clapped over it almost automatically.

"Make a noise and this stays dislocated for the duration of our 'chat'; stay quiet and I put it back," a voice practically growled in Kavanagh's ear. "Clear?"

After Kavanagh managed to collect himself enough to nod, he was treated to another sharp burst of pain as his arm was reset- there'd be some sore ligaments, but from what he could tell it didn't _feel _like his arm was going to have any severe damage as a result of what had just happened to it- before the attacker casually sat down opposite him, revealing a masked face that Kavanagh instantly recognised.

"_Phantom_..." he whispered, his face growing pale almost automatically.

"Bingo," the Phantom replied, in that low, slightly guttural voice that had left Kavanagh so uncomfortable the last time he'd heard it. "Now then, let's cut to the chase; what is your connection to the Trust?"

"I don't _have-_" Kavanagh began.

"You have an extremely low opinion of Elizabeth's way of doing things, you favour methods that would endanger _others _over methods that might put you yourself at risk, you definitely have the technical knowledge to modify the Atlantis failsafes to set up our current predicament involving the ZPM being set to potentially overload if too much power is drawn from it at once, and when you factor in the fact that you were _very _eager to leave here when _Daedalus_ departed- to say nothing of the fact that the team searching for clues noted that you sent three encrypted messages to Atlantis on your way here-, well..." the Phantom said, his eyes narrowing as he stared at Kavanagh.

"So... what?" Kavanagh countered, trying to assert himself; he wasn't going to admit to being afraid of a renegade masked vigilante (Even if he _was _afraid of the guy; his arm still smarted from the dislocation). "I wanted to make sure a few friends were all right; you're just assuming I'm guilty until proven innocent-?"

"I'm _assuming _as such until you give me clear, concise evidence that you're _not _responsible for our current situation, and so far your current attitude does little to make me think otherwise, particularly when you just said that you were trying to send messages to your friends here after saying earlier that you left because you didn't _have _any," the Phantom countered, standing up and leaning over the table to glare at the other man. "So, either start cooperating- I might be willing to assume you were exaggerating your social status earlier for dramatic effect-, or learn just how much damage and pain the human body can endure without any _serious _damage being caused to any part of you..."

"You wouldn't," Kavanagh said, staring coolly back at the Phantom. "You put too much value in Doctor Weir's opinion; did you think I wouldn't realise _why _you went to the bother of threatening me to edit my message back to Earth? You _need _her to-"

A sharp kick to the right kneecap left Kavanagh momentarily screaming in pain before the second kick knocked the kneecap back into place, the pain shifting to a lower-but-still-noticeable level as the Phantom glared at him.

"When it comes to the safety of Atlantis," the Phantom said, his eyes narrowing as he looked at Kavanagh, his fingers tapping slightly on the table before him as though he was itching for an excuse to attack the man before him, "I can assure you that little details like one woman's opinion of me matter _very _little... particularly when I am dealing with someone who has already provided me with ample evidence to lead me to the conclusion that he would welcome the Trust's method of doing things so long as he was absolutely certain that he himself would be at no risk."

"You psychotic-!" Kavanagh began, still clutching at his throbbing knee.

"Your insults mean little to me, and your threats even less," the Phantom said simply. "I will say this again, Doctor Kavanagh, and this time I expect a clear answer or we'll move on to seeing just how much damage I can do to your fingers without breaking anything; _did you plant the code in Atlantis's computers_?"

"_NO_!" Kavanagh screamed, as the Phantom reached under his cloak and pulled out his gun. "I didn't do it; I didn't do _anything_, I just want to get out of this psychotic facility that allows an overly emotional woman to use a deranged _lunatic _as-"

The sound of the Phantom's gun being fired was the last thing Kavanagh's senses registered before he was rendered unconscious.

* * *

"He didn't do it," John's voice said as Elizabeth stood in the control room with her senior staff, the team going over the various lines of code to try and determine the most effective means of reactivating the failsafes.

"Excuse me?" McKay asked, turning from the screen where he and Lieutenant Cadman were going through the various lines of code to look at the masked man uncertainly. "Who didn't do what?"

"Kavanagh might be a prat, but he didn't shut down the ZPM failsafes," John said by way of explanation, his tone brisk and his arms folded in a manner that made it clear that he wasn't that interested in discussing the current topic in greater depth than he had to. "I... gave him good reason not to lie to me, and then I stunned him; he should be out of the equation for now and we can focus on the more immediate matter of finding the code."

"And you're _sure _he's innocent?" Sumner put in, his eyes narrowing as he looked at the man he had formed an unwilling alliance with. "I'm sure I don't need to remind you that time is a crucial factor right now-"

"As I said, I gave Kavanagh a good reason not to lie to me," the Phantom replied (When John was this direct, Elizabeth couldn't entirely bring herself to think of him as 'John'; this was the Phantom that had made the Wraith afraid, not the man who'd risked everything to save Atlantis). "Trust me; he's not the man you're looking for right now."

"Well, given that he was pretty much our prime suspect because _you _suggested he was, that doesn't leave us with a lot of options right now!" McKay said, waving a frustrated arm at the Phantom even as he returned his attention to the computer screens before him. "I've been going over everything we've _got _and I'm _still _no further along in cracking the code to get those failsafes back up and running, and those Wraith cruisers are just getting closer..."

"Uh..." Lieutenant Cadman said, looking uncertainly back at the rest of the senior staff. "Actually, I _did _notice something that might be relevant earlier."

"Such as?" McKay asked with an impatient glance over at Cadman.

"Well, when I was going over the communication logs for _Daedalus_, apart from some encrypted messages from Kavanagh that we're still working on, I noticed some anomalies in the system command logs from the last few months," Cadman said, looking slightly uncomfortably at the stares she was receiving from Sumner and McKay. "There's a couple of gaps in the data streams from a few weeks ago; it's probably nothing..."

"If something's been deleted from the records at that time frame, it _could _have what we're looking for," Elizabeth admitted with a thoughtful nod.

"Do we _really_ have to-?" McKay asked.

"We have enough time before those cruisers get here to explore that possibility; if this could turn up anything about who's responsible for this, we have to explore it," Elizabeth said, nodding resolutely at the young explosives expert. "See what you can turn up with that; in the meantime, Doctor McKay can continue searching for the code."

* * *

Standing in the conference room a couple of hours later as the Wraith cruisers continued to approach them- the _Daedalus_ was still waiting near Atlantis in the event of an evacuation becoming necessary if they were forced to raise the cloak-, Kavanagh having been taken to the infirmary to recover, Elizabeth was surprised that she was more apprehensive about the current confrontation than she was about who she was in the room with, even after witnessing the evident issues both men had with each other.

Colonel Sumner and the Phantom might be looking at each other from either side of the conference room table as though they were each waiting for the other to give them an excuse to start fighting- Doctor Beckett's report that Kavanagh's arms showed signs of dislocation had done little to Sumner's opinion of the Phantom; Elizabeth was almost certain that John had lost much of his previously-gained credibility with that action-, but she was nevertheless confident in their ability to handle the current problem with a reasonable degree of control regardless of their issues with each other.

If anything, she was almost disturbed at herself at how willingly she'd accepted the news of what John had done to Kavanagh. She didn't condone torture herself, of course, but she could see how John might have felt that it was necessary to resort to those methods in the first place, and it wasn't like they hadn't had good reason to assume that Kavanagh had been up to something; so long as he hadn't caused Kavanagh any actual permanent- or even seriously long-term damage-, she couldn't bring herself to feel that concerned about what had taken place...

The transporter activating and depositing Colonel Caldwell in the room with them cut off any further self-analysis Elizabeth might have been planning to make regarding her feelings about what John had done to Kavanagh; right now, a saboteur had to be questioned.

"What the hell's going on here?" Caldwell said, looking in admittedly very convincing confusion at the people around him as he stood up to face her more directly (John had already moved back into the corner of the room, Elizabeth noted; evidently he wanted to be out of immediate range of any attack but also be ready to act if he had to).

"I asked Hermiod to beam you here so that you could give us the access code," Elizabeth replied.

"_What_?!" Caldwell said incredulously.

"Lieutenant Cadman discovered a gap in the system command logs that indicated two deletion points that she had-" Elizabeth began.

"Look, we don't have _time _for this!" Caldwell protested, glaring between Atlantis's two commanders.

"_Your_ identification code was used to identify this city's operating system," Elizabeth continued as she walked forward, ignoring the indignant expression on Caldwell's face. "_You_ copied it and took it back to The Trust, whose Goa'uld scientists then rewrote the programme to overload the ZPM. _You_ then brought it back here and uploaded it into the Atlantis computers."

"You think I'm working for the Trust?" Caldwell asked, a slightly stunned, incredulous smile spreading across his face that made it clear that he couldn't believe what he was hearing.

"We _know _you're working for the Trust," Sumner informed his _Daedalus _counterpart, drawing his sidearm from its holster and cocking it. "Give us the code and this doesn't have to get ugly-"

The sudden golden gleam of Caldwell's eyes instantly halted any thoughts Elizabeth might have had of simply reasoning with him.

Caldwell was a Goa'uld host...

"_**I will never give you that code**_," the creature using Caldwell's body said, using the same dual-toned voice that Elizabeth had heard far too many times during her failed 'negotiation' attempts during her few short months in charge of the SGC.

"_**I warn you**_," Caldwell's Goa'uld continued, even as Sumner raised his pistol to aim it at the other man's head, "_**as a Goa'uld I now possess the strength of many men**_."

"Nice threat," John said, prompting the Goa'uld to turn around and face him as he walked out of his corner, Elizabeth taking a few quick steps back to avoid any chance of being caught in the seemingly-inevitable crossfire. "Too bad this isn't the kind of fight where that kind of advantage counts for anything."

Before Caldwell- or at least the creature now inside him- could respond to that statement, John had kicked his opponent in the chest with such force that even the Goa'uld-enhanced host was knocked to the ground, promptly pulling a taser gun out of his cloak and firing the electrodes at the man's chest, leaving Caldwell tensed in pain as electricity pulsed through his body, his eyes briefly flashing as John briefly turned the voltage off only to turn it back on again.

"Hold on, you-!" Sumner began, only for John to shoot him a brief stare that made it clear that arguing would accomplish nothing as he continued to send the taser's power through Caldwell's body for another few seconds until he turned it off, leaving the _Daedalus _commander weakly groaning in pain.

"Colonel Caldwell?" John said as he looked at the man before him.

"Yes..." the man gasped, looking weakly around him, grimacing at the pain in his body from the taser assault.

"Good," John said, stepping back and nodding to Sumner. "Your cue now, Sumner; I'm out of here."

Before Sumner could even open his mouth to protest, John had turned around and hurried out of the conference room, leaving Elizabeth and the colonel to simply exchange brief glances before Sumner crouched down alongside Caldwell.

"We're running out of time, Steven," he said, looking urgently at his _Daedalus _counterpart. "We need the ZPM access code; can you tell us what it is?"

* * *

A couple of hours later, Elizabeth stood silently on her balcony, staring reflectively out at the sea before her.

In the end, she couldn't deny that things had worked out a lot better than they might have done. Thanks to the access code they'd acquired from Caldwell's Goa'uld, the ZPM failsafes had been restored in time for them to safely activate the cloak and leave the distress beacon on the continent to give the impression that the signal had merely been a last remnant of Atlantis that had activated by sheer chance rather than deliberate action, and Caldwell's Goa'uld had been safely extracted from him by Hermiod using the _Daedalus _transporters.

The only problem with the current situation, in Elizabeth's opinion, was that Sumner's already-shaky opinion of John had been further damaged by his perceived-excessive treatment of Kavanagh; the fact that Kavanagh had turned out to be innocent after John had temporarily dislocated some of the scientist's limbs- particularly given that he went on to _shoot _the man, albeit just to stun him- did little to convince Sumner that John could be trusted as anything other than a potential rogue element with an unpredictable temper.

The fact that she wasn't that concerned about it herself was actually the most worrying thing about it all; when had she reached the point where she was _that _willing to excuse whatever John did regardless of how... brutal it was?

He might not have actually caused _permanent _harm to Kavanagh, but he'd still resorted to methods that she wouldn't have condoned under normal circumstances; what was it about John that inspired so much... _faith_... that he was a good person when she constantly saw him display such a casual attitude towards physical violence with such limited- practically non-existent- knowledge of the history that had led him to assume his current role?

Had her time on Atlantis changed her so much that she considered what John did... acceptable?

_Great_... Elizabeth groaned. _Here I am, a whole _galaxy _away from Earth, having almost completed my second year of command, and _now_ I start questioning my judgement about my reliance on this guy_...

Maybe Sumner was right; maybe John _was _too unpredictable to be allowed the kind of free reign of Atlantis that he'd enjoyed so far...

Capturing and containing him for questioning about Atlantis might be an extreme response, but maybe she should consider trying to talk him into maintaining a more... active contact with the military personnel of the city, rather than just his current role of dropping in to help out when he wanted to how he wanted to...

It would be the smart thing to do; John's actions in interrogating Kavanagh, no matter what kind of suspicions they'd had about him, had crossed a line that Elizabeth had always promised herself nobody would be permitted to cross in Atlantis...

So why did she still feel so reluctant to judge John based on his more ruthless moments?

* * *

AN 2: Next chapter jumps- with looks at the intervening episodes, I assure you- to one of those episodes that I'm sure all ShWeir fans enjoy; the Phantom-ised take on "The Long Goodbye"...


	15. A Moment of Truth in the Lies

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Mystery of the Phantom

Looking over the paperwork spread out in front of her, Elizabeth had to admit that she was impressed at their recent progress in Atlantis. The recent discovery about those whale-like creatures in the planet's oceans definitely raised some interesting possible avenues for future scientific research- she might want to consider bringing in a couple of marine biologists at last; she'd thought about it when they'd first learned that the Ancient city was Atlantis, but had decided against it at the time given that they'd had no way of knowing how accurate the legend was and nothing noteworthy had been found in the sea until now-, their recent contact with the Tower had given them a fully-restocked supply of drone weapons and gateships, and the last few survey missions had generally gone relatively smoothly...

In the end, however, all this work didn't change the fact that Elizabeth still had to get around the fact that she had yet to come to any decision about her issues with the Phantom.

The events of the Trust's attempt to blow up Atlantis might have left her questioning his methods, but that didn't change the fact that he'd still come through for them when it _really _counted; she could hardly question whether he'd prove to be a danger to them at some point in the future when they'd spent almost two years here so far and everything that he'd done had only been to their benefit...

What _was _it about John that constantly left her feeling as though he had a good reason for even his most questionable actions? She tolerated Ronon's occasional moments of brutality- she was fairly certain that he would have been ready and willing to use physical violence to continue the interrogation of the now-departed Kavanagh if John hadn't been available-, but that was because she knew what had happened in his past to drive him to that point, and even then she couldn't help but feel wary about him; with John...

She might be uncertain about his past, but somehow, she couldn't imagine what she'd do if he proved to be dangerous to the rest of the expedition simply because she couldn't conceive of a situation where he _would _be dangerous to them.

Even when they found further reports of what he'd been doing on other planets before their arrival, they seemed to support her idea of John as a man who recognised when taking _no _action was more helpful than taking the wrong one. The recent incident with the Lord Protector, for example, had included the former 'prince' of the planet mentioning that 'the Phantom' had shared the expedition's objections to the current social structure, but he'd left them alone after failing to change their minds about anything.

It might have been her own... friendship... towards him influencing her assessment, but personally Elizabeth couldn't help but see that as an encouraging example of John's attitude; when he'd failed to make the Lord Protector change, he'd left the situation alone so that the people could still be protected (The expedition might have made some changes themselves, but there was a difference between being an extremely skilled fighter and having the kind of resources possessed by the SGC available to you)...

"Doctor Weir?" Chuck said from the door, prompting Elizabeth to break off her train of thought- something she had to admit was probably for the best; she was starting to risk approaching dangerous territory if she continued thinking for much longer- and look up at Atlantis's head 'gate technician. "We've just received word from Colonel Sumner's team; they've found something that you might be interested in."

Pushing the forms before her off to the side, Elizabeth stood up and followed Chuck, hoping that whatever she was about to learn would at least prove interesting; after everything else that had been going on in Atlantis recently, they could use a decent intellectual puzzle rather than an obviously dangerous one...

* * *

As he sat in his usual 'resting place' in the Atlantis repair tunnels- as much as anywhere in the tunnels could be said to be somewhere that he could rest; they weren't exactly built for long-term habitation even without the fact that he had to constantly monitor what was happening in the main city in case one of Sumner's search parties ever came close to finding his current location-, John silently listened to the current conversation taking place in the lab, Elizabeth's radio having been activated after she'd left her office so that he could be aware if anything turned up that he should know about.

He had to admit, the concept of these 'stasis pods' that Sumner's team had discovered was enough to intrigue him just as much as anyone else, and the expedition could definitely use allies with the Wraith still building up power in the galaxy, but he couldn't help but feel at least slightly uncomfortable about the whole thing; encounters with the likes of the Genii and Halcyon didn't exactly encourage you to hope for the best when dealing with advanced civilisations in this galaxy.

Of course, Caldwell's presence on Atlantis while _Daedalus _was away didn't exactly make him feel particularly comfortable, although that could just be because it was the first time Caldwell had spent any kind of time in the city since he had his Goa'uld extracted. He respected the man's desire to make up for what the Goa'uld within him had done before it was exposed, but that wouldn't stop him being a bit on-edge; it might just be because of his limited knowledge about them in the first place- the Elizabeth he'd first met had been more focused on telling him about what he might confront in the Pegasus galaxy rather than talking about what the SGC had dealt with back home, and he hadn't had the time to find out anything more detailed about them since then-, but he just found it hard to be comfortable around the guy...

"..._alive- barely_," Doctor Beckett's voice said, drawing John's attention back to the conversation taking place in the lab; he couldn't see the location himself- there hadn't been time to move to that area and it didn't sound like anything was going to happen to Elizabeth there that required her attention-, but it sounded like they'd opened the pod they'd discovered already. "_It appears we found her very near the end; all the major organs are shutting down_."

"_How long was she out there_?" Elizabeth asked, her voice a low, astonished hush.

"_There's no way to tell for certain_," Doctor Beckett replied.

"_So she _could _be an Ancient_?" Elizabeth asked.

"_Uh, the pod design makes me doubt that_," McKay replied, evidently sceptical, prompting John to dash that possibility from his mind; McKay might be arrogant, but he knew his technology well enough to know whether or not something was Ancient.

"_It's a shame she can't speak with us_," Elizabeth continued. "_Just imagine what she could tell us about her people and about what happened to her_..."

After a moment's pause, John heard a sound like something activating, followed by the sound of someone falling and McKay calling out Elizabeth's name.

"Medical team to Lab Three, stat!" Beckett called out, confirming John's worst fears but simultaneously leaving him with nothing to do but sit apprehensively in his small corner of shaft as he listened to the subsequent hustle as Elizabeth was hurried off to the infirmary, John only able to briefly register the rest of the panicked confusion taking place in his ear as he waited for some sign that Elizabeth was all right.

She had to be OK... she _had _to be fine... he couldn't have been so careless as to let her get killed in a stupid accident like _this_... it was just a damn pod, just a simple routine thing...

* * *

"This_ is not my fault_," McKay's voice protested, the Canadian's annoying tone serving as a strange source of comfort for John as they drew him out of the panic that had been dominating his thoughts since whatever had happened to her had happened. For all of McKay's faults, he wasn't insensitive; if he felt that the time was right for him to be talking like that, then Elizabeth was probably past the worst of whatever had happened to her.

"_We were all there, Doctor; we know what you were and weren't responsible for_," Sumner said, his tone inspiring more reassurance in John than McKay's. McKay might have confirmed for him that Elizabeth was past the worst of what was happening, but Sumner's tone made it clear that he was willing to make sure McKay recognised that he'd been an idiot to let Atlantis's leader be in such close proximity to an unknown alien device...

"_She's coming around_," Beckett said, giving John a brief moment to sigh in relief at the sound of footsteps as people moved to (Presumably; he'd been so focused on listening for news of Elizabeth's condition that he hadn't been able to bring himself to head to the medical bay to check on her himself).

"_Are you all right, Doctor Weir_?" Sumner asked.

"_Doctor Weir is fine_," Elizabeth's voice replied in a slightly bland tone.

Instinctively, John found himself tightening his grip on the gun he hadn't even realised was now in his hand; even without the fact that he'd been thinking about the Goa'uld earlier, that choice of wording _definitely _didn't sound entirely encouraging...

"_I take it from that comment that you are _not _Doctor Weir_?" Sumner said, a faint sound suggesting that he was arming a weapon while trying not to be obvious about it.

"_She was simply overcome by the effects of the imprinting_," Elizabeth's voice replied with a nonchalance that John himself wasn't feeling at this point.

"_Security team to the infirmary_," Caldwell said, along with a slight tap that sounded like he was activating his radio (Not that John could know for certain; he was currently 'tapping' into Elizabeth's radio rather than Caldwell's, after all).

"_That's not necessary, Colonel... Caldwell_," Elizabeth's voice said reassuringly. "_She is... merely harbouring my consciousness_."

"_And you are_?" Sumner asked (John thought he heard McKay muttering 'again', but concluded that it wasn't important; what mattered right now was what had happened to Elizabeth _now_, not pondering the similarities to things that had happened in the past).

"_I am Phoebus_," 'Elizabeth' replied. "_We are a race of explorers. On our journey home our vessel was attacked_."

"_By the Wraith_?" Caldwell asked.

"_Yes_," Phoebus replied (John couldn't think of her as Elizabeth even if the voice was the same; it wasn't _Elizabeth_ where it really counted). "_We were forced to abandon ship and launch our life pods. If this has happened to me, then I've been adrift for some time and the pod has determined my body is beyond resuscitation_."

"_You're quite correct_," Beckett said apologetically.

"_Then, for all intents and purposes, I am already dead_," Phoebus said, her tone a simple, direct one that gave no indication about her feelings on the matter.

"_I'm sorry_," Beckett said.

"_So am I_," Phoebus replied simply.

"_Getting past that issue, would you mind clarifying what happened to Doctor Weir when she began... harbouring your consciousness_?" Sumner asked.

"_She is here also_," Phoebus replied, even if that statement did nothing to assuage John's concerns about what had happened to Elizabeth in this whole mess.

"_And I suppose you'd like us to take your word for that_?" Caldwell asked, neatly voicing John's own concerns about the current situation; after their experiences with Caldwell's Goa'uld, anything that used another person's body like its own was unlikely to easily win their trust.

"_Would you like to speak to her_?" Phoebus asked nonchalantly.

"_If you can_," Sumner replied, followed by a brief pause before Elizabeth sighed again.

"_Doctor Weir_?" Caldwell's voice said once again.

"_Oh_!" Elizabeth said, her voice now demonstrating more emotion than Phoebus had previously. "_Oh, it's OK, Carson, I'm- I'm fine_."

"_Doctor Weir_," Sumner said, "_I have to inform you that_-"

"_I know_," Elizabeth replied casually. "_Her name is Phoebus_."

"_You seem remarkably... sanguine about all this_," McKay put in, addressing John's obvious concern about this; after the Goa'uld, he'd have been very uncomfortable with _anything _living in his head.

"_Well, the imprinting will only last a matter of hours_," Elizabeth clarified, before she continued. "_The other pod – Phoebus urgently desires to be here when we bring the other pod back to Atlantis_."

"_Why_?" Sumner asked.

"_She believes it's her husband_," Elizabeth responded, her voice sounding almost amused at the prospect.

"_Husband_?" Caldwell repeated, John only just stopping himself repeating the word himself, his mind distracted from his previous thoughts of Elizabeth's odd word choice; something about that sentence- and, now that he thought about it, the tone of the last one- hadn't sounded quite right...

"_He escaped the ship- she's certain of it_," Elizabeth explained, sounding almost like a giddy schoolgirl as she spoke (John was _definitely _making sure she had a check-up after this; Elizabeth wasn't _meant _to act that way, she'd always been so _professional_...)

"_And, uh_..." she continued, laughing briefly as she spoke. "_The rush of emotion is... it's overwhelming_."

Even knowing that it wasn't really Elizabeth feeling the emotions that she was talking about- and that he had no actual _right _to feel that way- did little to help John quash the sudden stab of jealousy he felt at that last comment; the prospect of another man inspiring that kind of... emotion... in Elizabeth was something he didn't like to consider in depth.

"_Actually_," Elizabeth continued after a momentary pause, "_on the topic of emotion, Phoebus has a favour she'd like to ask you, Colonel Sumner_."

Once again, John fought back an irrational jealousy as he processed the implications of what he was hearing; he had _no right _to have any kind of say in who Elizabeth did or didn't... have feelings for... no matter whether or not he thought that Sumner was a git without any real improvisational talent...

If she was happy, he could accept that; that was _all _that mattered...

* * *

"As I understand it," McKay said an hour or so later as they stood in the lab with Phoebus's pod once again, the pod containing her alleged husband now in the room as well- taking advantage of the time needed to pick up the pod and bring it back, John had crawled over to a tunnel near the room so that he could make sure the transference progressed safely, even if he was already resolved to depart if anything... happened... between them-, "the beam that hit Elizabeth was part of a failsafe feature built into the pod system. As cellular failure progressed, the pod stored her consciousness in a sort of, uh... flash memory."

"Why?" Caldwell asked. "I mean, what good is the technology if the effects are temporary?"

"A black box equivalent seems the most obvious possibility," Sumner speculated. "If the bodies themselves can't be recovered, the minds would at least be able to report what happened to the ship and allow the rescue team to determine what had happened."

"A human flight recorder..." Caldwell muttered, shaking his head as he studied the pods. "That's pretty dark."

"Maybe, but it's also useful in times of war," Sumner pointed out.

"As well as for giving two survivors the chance to say one last goodbye, mmm?" McKay added, smiling at Sumner just as Doctor Beckett arrived, Elizabeth/'Phoebus'- John had no way of knowing who was in control at this point- sitting in a wheelchair in front of him as her eyes automatically focused on the pod before them.

"Are you sure she's up for this?" Caldwell asked as Elizabeth/'Phoebus' got out of the chair to step closer to the pod.

"Physically, she's perfectly fine," Beckett said (John wished the guy had said that it _wasn't _OK; even if Elizabeth wasn't going to be the one doing it consciously, her body was still going to... do _that_... with someone...). "Besides, Elizabeth wouldn't take no for an answer."

"Love is a powerful thing, Carson," Elizabeth said in a low voice as she studied the pod.

"You're a hopeless romantic, aren't you, Doctor Weir?" Sumner said, the other man smiling slightly as he looked at her.

"Well, _you're _just as hopeless, otherwise you wouldn't have agreed," Elizabeth responded with a smile.

"It was a dying woman's last request, Doctor Weir," Sumner replied with a brief shrug, the slightly nostalgic smile on his face one of the few true signs of emotion John had ever seen the man express. "That's not something you can turn down."

"Besides," Doctor Beckett added, "from what I've been able to determine from going over the respective EEG patterns, I can say with some degree of confidence that this... 'imprinting'... as Doctor Weir's temporary occupant calls it, won't last more than a few hours."

"You can guarantee that?" Caldwell added (John actually found himself agreeing with the other man for what seemed like the first time since he'd first seen him; the last thing he wanted was Elizabeth playing host to a technological 'ghost' on a long term basis).

"A day at most," Beckett confirmed.

"Well, I'm sold," McKay said, looking around at the others before indicating the still-sealed newly-arrived pod. "Shall we?"

Without waiting for a response, he pressed something on his computer tablet and the pod lid slid open, revealing an elderly man in a brown uniform of some kind.

"He's still alive," Beckett said after a brief glance at his scanner, Elizabeth staring at the old man with a slightly tightened expression. "Same as before. Life signs even fainter than the first one. If we're going to do this, we should do it now."

"Take this," Sumner said, unstrapping his pistol and handing it over to McKay. "Whatever else is happening here, I'd prefer it if my body wasn't armed in this situation."

Nodding briefly in acknowledgement, McKay took the offered weapon, Sumner subsequently taking a brief step towards the pod before he turned to look at Elizabeth.

"If anything... _happens_... between them, Doctor Weir," he began, looking as close to being uncomfortable as John had ever seen the colonel in question, "I want to assure you-"

Elizabeth cut him off mid-sentence as she held up her hand and lowered her head, taking a deep breath before raising it again, this time with a slightly different expression on her face that suggested to John that control of her body was once again in Phoebus's metaphorical hands.

"I promise to be discreet, Colonel," she said simply (John _really _wished he could put away the mental images implied by that statement; the slightly seductive tone she used at the time didn't exactly help matters).

"Well..." Sumner said, taking a deep breath as he looked at the pod. "See you all later."

With that, he walked up to the pod and leaned over it, a white beam shooting out of the pod to envelop him almost instantaneously, Phoebus subsequently holding out a hand to halt Beckett's attempt to approach the colonel as Sumner swayed slightly unsteadily on his feet.

"Give him a moment," she said, patiently watching Sumner as he stood by the pod, his head lowered, until his head snapped up, his eyes open and automatically fixing onto her.

"Thalen?" Phoebus said, smiling slightly at him. "It's me."

"Phoebus?" 'Sumner' replied uncertainly.

"It's all right; these people recovered our pods," Phoebus replied, as she began to walk around the pod towards Thalen. "We may well be the very last of our kind; these... generous people have allowed us to be together one last time."

"You consented to this?" Thalen asked, looking over at Caldwell, apparently identifying him as the authority figure in this situation.

"One last chance to say goodbye," Phoebus replied with a brief smile. "It seemed... appropriate... to use these bodies for that purpose, given the... relationship between them."

For a moment, John's fists automatically clenched at the implications of what he'd just heard; the thought of Elizabeth and _Sumner _having the kind of connection that he'd longed to have with Elizabeth for longer than he could even remember...

_STOP IT_! he mentally berated himself, pushing that thought to the side as hard as he could.

It wasn't worth thinking about things like that; no matter how much he might like to dream otherwise, those thoughts would bring him nothing but heartache and frustration if he ever tried to act on them.

_So long as Elizabeth was happy_...

"I know this body is different," Phoebus continued, "but I assure you, Thalen, it's me."

With that said, she turned her attention to the others even as she continued to face the man who had once been Sumner. "Is it possible for us to be alone, just for a few minutes?"

"No, absolutely not," Caldwell said. John couldn't help but feel briefly supportive of Caldwell in that moment; even without his jealousy issues, the idea of Elizabeth's body doing something like... this... when she wasn't in control of it...

Even if she'd consented to letting Phoebus remain in control, it still _felt_ like rape to him...

"Don't be so heartless!" Beckett said, looking over at Caldwell with a slightly scolding tone.

"They are two consenting adults!" McKay added in exasperation.

"That's not what I'm concerned about, Doctor," Caldwell said (John just wished he could convince _himself _that the city's security was all that he'd been concerned about in that moment...).

"The Colonel's right," 'Thalen' said briefly.

"Doctor Weir is in charge of this facility," Phoebus added, looking uncertainly at him.

"I'm just saying, there should be an armed guard just outside the door," Thalen continued.

"Two guards," Phoebus added, her eyes flicking briefly over to look at the colonel. "One in _each _door."

"I've already taken that precaution," Caldwell put in. "They're right outside."

"Of _course_ they are," Phoebe said, she and Thalen exchanging brief smiles.

Before anyone could stop them, the two leaders of Atlantis- the fact that they were in the leaders' bodies was the only thing saving them from being shot at this point, in John's opinion- suddenly turned and ran towards their nearest doors, McKay's startled yells ignored as Thalen and Phoebus both swiftly rendered the guards unconscious and stole their Wraith stunners, Thalen swiftly taking Caldwell out with his stunner as Phoebus hid behind the other door. The evidently-panicked McKay drew the gun that Sumner had given him and tried to fire at the possessed colonel, only for Thalen to turn and run off down the corridor as Phoebus walked back into the room, her stunner aimed at him.

"You two need some _very _serious marriage counselling-!" McKay began.

"He's not my husband; he's the enemy," Phoebus replied, confirming John's assessment that there was something else going on here, her tone giving the impression that McKay was an idiot for not realising the truth sooner. "Drop your weapon."

Lacking alternatives, McKay dropped the pistol to the ground.

"Now radio security and tell them everything is fine," Phoebus continued, unaware of John pulling out his gun and shifting it into stun mode as he prepared to exit his small observation point.

It wasn't something he'd _like _to do, but if it meant stopping Elizabeth's body being used to do something that she herself would _never _condone...

He aimed his gun at her, his body tenser than it had been when he first began his journeys through the Stargate- even after all the training he'd done there was no way to _know _how you were going to be able to cope with something as dangerous as what the old Elizabeth had told him about the Wraith-, waiting for the moment when he could shoot her... she'd stunned Beckett for speaking, but he was still all right... McKay was making a transmission to 'confirm' that everything was fine... Elizabeth's body was contained, she wasn't going to do anything...

"Oh, forget it," Phoebus said, casually stunning McKay as he continued to talk incessantly in a manner that wouldn't have convinced anyone, before she walked over to the fallen scientist and took his headset for herself.

"This is Doctor Weir," she said, the same cool authority that had always drawn him to Elizabeth somehow instinctively perverted as she picked up a gun along with her stunner. "Attention all personnel. Colonel Sumner is not, I repeat, _not_ who he pretends to be. If you find him, secure the area and contact me immediately; I'll deal with him myself."

_Damnit_... John thought to himself as Elizabeth walked out of the lab, leaving him staring in frustration at the suddenly-empty room before him, filled with nothing more than unconscious soldiers and doctors as their possessed commanding officers headed out into a city that had no idea what had happened to them and were equally ignorant of what they were up against.

There was nothing else for it; he'd have to backtrack to somewhere that would allow him to exit the tunnels- his current location was good for taking pot shots at the people in the room but he couldn't have actually _entered _the room to take a more physical role in things from this point-, and hope that he could find Phoebus or Thalen before they did something Elizabeth or Sumner would regret...

* * *

AN: Well, hope that was worth the wait; next chapter will be told primarily from Phoebus's POV, so anyone with any suggestions to make about information from her past- theories about the reasons why her and Thalen's people were at war, things like that- would be appreciated; I've got a couple of ideas, but with so little _definite _information about them suggestions wouldn't go unnoticed


	16. The Masks We Wear

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This begins shortly after the end of the last chapter, with Phoebus having already made contact with Lorne's team and convinced them that she's still Elizabeth; Thalen's role at this point will be pretty much the same as it was originally, but things get more interesting for Phoebus when she's about to take out Lorne's team...

Mystery of the Phantom

As Phoebus walked through the corridors of Atlantis, she almost couldn't believe how easy this had been so far; for soldiers, these people had no _real _evident concept of warfare. She'd been in control of Elizabeth Weir's body for almost half an hour already- not counting the time she'd spent feigning that Weir was back in charge to trick them into giving her what she wanted-, and not only was she still uncaptured, but she'd actually successfully managed to convince an entire team that she was still Elizabeth Weir...

Quite frankly, she was almost tempted to shoot them after she'd finished dealing with Thalen; she'd be doing them a favour getting rid of such pathetic soldiers. Obeying orders was good, but there was a point where you needed to recognise when you were obeying the _wrong _orders; the number of times she'd nearly been killed because a couple of commanders had defected...

"You know," Major Lorne said as they ran through the corridors of Atlantis, Phoebus grimly leading the way, "it would help a lot if we knew more about what was going on."

Phoebus didn't bother to respond to that; if push came to shove and they continued to insist on an explanation, she'd just say that there wasn't time to worry about that sort of thing when they were dealing with a hostile life-form...

"_This is Caldwell_," a voice suddenly said over her host's radio. "_Both Doctor Weir and Colonel Sumner are under the influence of alien entities. If at all possible, subdue and contain them with non-lethal force_."

_Damnit_... Phoebus reflected, coming to a halt as she turned to look at the small team she'd tried to bring together. _So much for things being this easy_...

"Ma'am!" Lorne said, he and his men arming their guns as they moved to surround her. "I'm going to need you to hand over that weapon."

"Did it occur to you that Colonel Caldwell might be under the same influence as Colonel Sheppard?" Phoebus asked, trying to sound as diplomatic as she could based on Elizabeth's memories (She was a soldier, not a diplomat; she resorted to talking only when there was no direct way to get what she wanted). "You weren't there."

"Hand over the weapon, now," Lorne said, refusing even to acknowledge the possibility of the scenario she'd just proposed; even if Lorne did have doubts about the current situation, he was evidently still going to take her into custody to make sure.

As one of the men reached for her weapon, Phoebus prepared for her chance to attack; given that they weren't expecting 'Doctor Weir' to be capable of fighting back against them, if she could just time it correctly-

Before she could even move, the four men around her suddenly rapidly fell to the ground, one after the other, surrounded by a burst of red energy that momentarily crackled around them before fading away.

"Sorry for interrupting your little 'fun'," a voice said from behind her, "but given that I know for a fact this thing won't cause any _serious_ potential long-term damage, coupled with the fact that I had no idea what _you _were going to do to them, it seemed like the best way to stop anyone getting seriously hurt."

Turning to look at the source of the voice, Phoebus's eyes widened as she took in the man standing there, his distinctive silver mask and long black cloak making his identity obvious even without Doctor Weir's memories to draw on.

"John?" she said, recalling the true name she had learned about from Elizabeth's memories. "What are you talking about; Caldwell's-"

"I watched the whole incident take place, _Phoebus_; don't try and bullshit me by claiming that you're not some soldier hiding out in Elizabeth's body," the man known to almost all of Atlantis as the Phantom said, his weapon shifting to aim in her direction. "I'll make this simple; before you cause irreparable harm to anybody in this city, you will _get out of that body_."

"I have no intention of _hurting _Elizabeth Weir, John-" Phoebus began.

"_Phantom_," the man countered, his eyes narrowing as he glared at her. "Only Elizabeth can call me 'John'."

Despite herself, Phoebus couldn't help but involuntarily smile slightly at the unexpected sense of pleasure what remained active of Elizabeth's mind felt at that declaration; her host might not fully understand what she felt for this man, but she _definitely _had strong feelings for him...

"Well... Phantom," she continued, walking forward slightly with a reassuring smile, "we don't have to fight; we want the same thing-"

"You're willing to use an innocent woman to fight your own war; I want to see you out of Elizabeth's body before she comes to any harm," the Phantom interjected. "I'm not seeing _what _we have in 'common' there..."

"We both have little reason to think well of Colonel Sumner," Phoebus responded, taking a certain pleasure herself in seeing the hesitation in the stance of the man before her as he took in her last comment.

For all of Elizabeth Weir's faith in the man before her as a noble hero with nothing more than a slight pre-inclination towards more violent solutions, underneath that mask he was little more than the beast who had so brutally tortured and killed those Genii soldiers during that attempted takeover of this city over a year ago...

"Keep talking," he said simply after a momentary contemplative pause.

"He holds the mind of the man who sought my death, and his presence in this city has constantly hindered your efforts to establish yourself as its protector," Phoebus continued, trying to assume a more relaxed, open appearance as she slowly walked up to the man before her, easing her way into his personal space without making her actions obvious. "You could do so much more if he was not here; once you establish that Atlantis doesn't require him to operate, you may even be capable of moving beyond your current role and assuming his own."

For a moment the Phantom simply stood in silence as he looked back at her, but the contemplative expression in his eyes made it clear that he was thinking over her current offer.

"You don't even have to let anyone else know that you helped me do it," Phoebus continued, still smiling reassuringly at him, taking full advantage of her host's pre-existing friendship with this man to put him psychologically off-balance however much was needed for him to agree to work with her. "I can take Doctor Weir's memories of these last few hours with me when the imprinting process comes to an end; you can tell her that Sumner gave you no choice _but _to kill him if you were going to save our lives..."

"I _don't_ kill-" the Phantom said weakly.

"And the Wraith that Elizabeth recalls you defeating died of what?" Phoebus asked with a casual shrug.

"They would kill me _whatever _I did; Sumner isn't himself right now-" the Phantom countered, his tone demonstrating a greater resolve than he'd shown previously.

"And what if you'd only had one weapon available to you and didn't realise what you'd grabbed until _after _you'd fired it?" Phoebus asked, indicating the various guns lying around them from where Lorne and his men had dropped them after they'd been stunned. "A simple enough mistake, isn't it; you grab the wrong gun in the heat of the moment, you regret what happened in the aftermath, there's nothing you can do to change what happened...?"

Once again, all the Phantom cold do was stare at her in silence, contemplation dominating what could be seen of his face as he studied her, before he allowed himself a brief, grim smile.

"A chance to get rid of Sumner with a ready-made excuse to do it, without any blame being attached to me?" he said, the smile broadening slightly as she nodded in confirmation of his summary. "It's _tempting_..."

"Do it," Phoebus said, looking earnestly at him. "You owe yourself this chance; take Sumner out of the equation, and the path to you becoming the true defender of Atlantis will be assured."

In response to her statement, the Phantom cocked his weapon and smiled at her.

"Give me a chance to take Sumner's weapons from him before we kill him, and this could work," he said to her. "The expedition are pretty good when it comes to forensics work; if we don't kill him with his weapon, the story won't fit and Elizabeth might be able to work out that we shot him with intent rather than out of a lack of choice."

"Of course," Phoebus said, smiling slightly at she turned to walk off with her new ally, already savouring the feel of Elizabeth's desolation as the image of her city's dedicated protector was shattered at this sight of his true corruption.

It was like it had been with Thalen's people, really; they'd set out trying to 'prove' that they could do better if they ran things themselves, and in the end all that they'd accomplished was proving that they were incapable of doing anything other than plagiarising the greatness of her people and passing it off as their own.

For all of Weir's efforts to convince himself that the Phantom was 'better' than what he appeared to be, at heart he was nothing more than a monster who used fine words to try and conceal what he really was...

Putting those thoughts to the back of her mind- the last thing she wanted was anything that gave the Phantom reason to suspect that she had something else in mind for him apart from what she had previously claimed-, Phoebus smiled briefly at her new 'ally' before she activated her radio.

"Weir to Sumner," she said as she walked along the corridor, the Phantom just behind her; given the already-existent tension between the two leaders- coupled with the psychological impact it might have on anyone in the city listening into their conversation-, it seemed slightly apt for her to use the names of their hosts rather than their own at this point. "I'm assuming you can hear me?"

"_Yeah, I can hear you_," Thalen replied with his usual casual tone (He could never bother to show much emotion in any situation; his inability to really acknowledge the threat she posed was something that had always frustrated her), "_but if we keep using these radios, it'll only help them find us_."

"We don't don't have much time, Thalen," Phoebus replied. "The imprinting is temporary and these people are going to try to stop us."

"_We've got all the time in the world, and there's only one or two of them I'm really worried about_," Thalen responded dismissively.

"We both want a shot at the same thing," Phoebus continued.

"_You mean each other_," Thalen replied, prompting a brief amused laugh from Phoebus; Thalen always had possessed an amusing knack for stating the obvious.

"And neither one of us will get that chance if you keep running," she countered, exchanging a brief glance with the Phantom to make sure he was keeping their current goal in mind; now that he'd committed himself to helping her, making sure she completed her mission was the only thing she wanted him to be thinking about right now.

"_You're the one that likes to run_," Thalen retorted automatically. "_My ship ran out of fuel before I could even get a clean shot_."

"That was my plan," Phoebus replied simply.

"_You didn't have a plan; you just wanted me dead_," Thalen said in response.

"Still do," Phoebus said, allowing herself a brief smile at the thought before she forced her expression back to normal as the Phantom looked over at her; her chances of convincing him to help her would be better if he thought that she fought out of necessity rather than letting him be aware of the sheer satisfaction she felt doing her job. "Once I see that look of defeat on your face for the last time, it's all over."

"_Are you referring to the look on my face when you rammed my fighter, making sure neither one of us would win_?" Thalen asked in his annoyingly casual manner. "_That was hatred, not defeat, Phoebus_."

"Is that any way to talk to your wife?" Phoebus asked with a slight smirk, only to be met with silence. "Thalen?"

After a brief silence, she decided that it wasn't important; there really wasn't anything more she had to say to him, after all.

"Run all you like," she said. "The moment I find you, you die."

"Were you _actually _married?" the Phantom suddenly asked from behind her, prompting Phoebus to look back at her current 'partner' as they continued to walk through the city.

"To Thalen?" Phoebus replied, nodding in confirmation. "At one point, yes, before we went our separate ways due to ideological differences; he saw things one way, and I saw them another."

She didn't elaborate, but the Phantom's lack of interest in asking for more information confirmed her opinion of him; he might _act _like he wanted to be independent, but in the end everyone wanted someone else to be in charge of them.

_And _that _is why Thalen's going to lose_, Phoebus vowed to herself. _He doesn't have _anyone _to give him orders now..._

As she and the Phantom approached one of Atlantis's many interior balconies, she slowed her progress for a moment, taking stock of her surroundings; unlike the narrow corridors, these areas of the city held far more potential for an ambush than what they'd been exploring previously, and she couldn't afford carelessness, particularly when the already-low lighting in the area suddenly dimmed even further.

_Thalen_, Phoebus mused grimly; most likely her 'dear husband' was trying to make it harder for anyone to find them.

Still... if he thought that would make it harder to find him, he had another thing coming; Doctor Weir's memories made it easy for her to recall the location of the central power room, which was the only location where he could have gone if he was going to pull something like this off. Glancing over at the Phantom, Phoebus gave a slight questioning shrug- she had to make it look like she was thinking to herself; if she was being spied on, she didn't want to give her 'partner' a reason to turn on her to save his pathetic 'image' in the eyes of Doctor Weir's troops-, to which the Phantom simply jerked his head slightly to the side before running up to the edge of the balcony and jumping off.

As Phoebus ran towards the balcony herself, she briefly thought that she saw something moving out of the corner of her eye further down the balcony, but she was over the edge and on the lower level so quickly that she doubted anyone had time to even properly register her presence, never mind the Phantom's (The man was an arrogant reminder of the rebellious attitude that had destroyed her planet, but he was _very _good at what he did).

As they continued to hurry through the city, occasionally pausing to avoid any soldiers they encountered in their search, Phoebus spared a few moments when she wasn't planning Thalen's demise to wonder just how the Phantom had acquired these skills of his. His movements seemed somewhat rushed at times- it gave the impression that he'd developed his style of motion as a 'spur-of-the-moment' thing and never bothered to focus on minimising his energy output-, but his intense focus on the task at hand was definitely something that even she couldn't help but admire, particularly when she considered that he lacked her own personal investment in the current mission; if he was this focused when something he valued _wasn't _at stake...

She shook that thought off before it could progress further as they hurried up some stairs- narrowly avoiding another group of marines-, before they walked into a smaller room that was apparently used as a storage area.

"Wait," the Phantom suddenly said, reaching out to halt Phoebus before she could walk more than a few paces into the room.

"What?" she said, tuning to look at the other man with a pointed stare. "Why?"

"Because, if Thalen went to the central power room earlier- and has a good idea where you are-, this is one of the better areas for him to cross if he wants to find you," the Phantom clarified, his voice a low whisper as he spoke. "It's a quiet enough location with minimal sensors or living quarters in the immediate vicinity; Sumner may not know as much about Atlantis as I do, but I'm reasonably sure he knows this."

"And if you're wrong...?" Phoebus began, only to trail off as she heard footsteps from the other end of the room. Quickly moving into position alongside a nearby pile of boxes- even if it wasn't Thalen she should still be ready to strike-, Phoebus trained her gun in the direction of the approaching steps, barely even registering the Phantom's location as he moved off deeper into the room.

All that mattered now was finishing the mission...

As the muscular form of Ronon Dex came out from around the corner, Phoebus began to pull the trigger, only to be beaten to the punch when the red light of the Phantom's gun hit Ronon first, sending him falling to the ground before her bullets could make contact. Before Phoebus could take in what had just happened, Thalen stepped out from around the corner as well, his gun aimed in her direction, only for him to be taken down with another shot from the Phantom's gun.

For a moment, Phoebus smiled at how things had just gone- she'd won her peoples' long war _and _proven that the Phantom was nothing at heart but another animal-, but then she noticed the slight but significant slow rising and falling of Thalen's chest and realised what had happened.

"You didn't kill him?" she said, turning to look at the Phantom, only for her voice to trail off as she saw the masked man aiming his weapon at her.

"No," he said, staring at her with a cold intensity that would have almost made her afraid if she hadn't experienced the last few years of her life facing similar glares. "Unlike you, I don't allow a few issues with people's decisions to provoke me into killing an otherwise good man."

"_What_?" Phoebus said, looking at the Phantom incredulously. "You think he's 'good'? He'd see you _locked up_-!"

"We disagree with how I do things; it's an issue, but it's not exactly something worth killing him for," the Phantom interjected, still staring at her. "Anyway, that's not the relevant issue right now; what _is _relevant is that you're the last one standing in that war of yours, so congratulations for winning and you can get out of Doctor Weir's body now..."

"_Winning_?" Phoebus spat, staring incredulously at the Phantom as she continued to keep her gun trained on him; bullets might not do much if he possessed that 'personal shield' device that Doctor Weir's memories had informed her about, but the fact that he was reluctant to shoot at her body might be enough for her to gain the advantage if she could make him drop his guard for the necessary moments. "As long as Thalen still lives, this is _not _over; I will _not _allow _anything _of him to survive-!"

"What _difference _does it make, Phoebus?" the Phantom countered, glaring angrily at her. "Your war ended _centuries _ago; I doubt _anyone _in this galaxy knows who won it! There is no _point _to this-!"

"I will _not _go knowing that _anything _from Thalen still lives!" Phoebus practically spat at the Phantom. "As long as even the _memory _of him remains, he may outlive me; I will _not _let this war end in a stalemate!"

"And what was so great _about _this war, anyway?" the Phantom retorted, his grip on his weapon tightening. "You spent your life fighting, and for _what_? Victory for a race that died off years ago?"

"All I have to look forward to is excruciating pain before I cease to exist in this body; if I can achieve victory for my people-" Phoebus continued.

"It changes _nothing_!" the Phantom yelled.

"And what do you consider the purpose of your fight against the Wraith?" Phoebus retorted. "You seek _their _destruction as surely as I seek Thalen's-!"

"I seek their deaths to save innocent people from being fed on by them; _that _is _not _the same thing as _this_!" the Phantom yelled in response. "Who won or lost this war doesn't matter-!"

"It matters to _me_!" Phoebus yelled, pulling the trigger and firing the weapon as she ran towards the Phantom, the bullets impacting harmlessly against his shield as he raised his weapon to counter her attack, only for her to have him pinned to the ground before he could fire, smirking at him as she felt his body betraying itself at the close proximity to her borrowed flesh.

"Well well well..." she said, smirking slightly as she looked at the man below her. "I take it I'm doing _something _right, am I?"

"You're not _her_-" the Phantom spat, only to cut himself off as he realised what he was saying.

"I'm not Doctor Elizabeth Weir?" Phoebus finished for him, still smiling at the man below her; it had been a while since she'd tried seduction to get what she wanted, but her victim's obvious attraction to her host was definitely helping to compensate for that particular shortcoming. "Maybe not, but think of it this way; I'm your _only _chance to get what you've wanted since the moment you saw her."

"I _don't_-" the Phantom protested, even as Phoebus placed her hands on either side of his face, giving her lips a brief, seductive lick with her tongue.

"Oh, you know you do... _John_," Phoebus said, smirking at him as she felt the force field fade away- evidently the Phantom's subconscious desire for her host was overpowering his attempt at nobility- as she placed her right hand on his unmasked left cheek. "You know you've wanted this for ages; do you think that Doctor Weir hasn't noticed? You think that she hasn't been thinking about this?"

"She _hasn't_-!" the Phantom growled, staring back at her, anger clear in his eyes even with the slight hint of guilt in them that suggested to her that the man below her was enjoying his current position more than he wanted to.

"Oh, she is..." Phoebus said, smirking as she carefully slid a couple of fingers underneath the mask...

"_Oh my God_!" she yelled, sitting back in shock as her fingers came in contact with something hard and smooth that felt almost exactly like the few occasions during a battlefield medical crisis when she'd witnessed someone with a fractured arm where the bone stuck out of the skin; it felt like there was _bone _underneath that mask-

"You lose," the Phantom said suddenly.

Phoebus only realised that she'd relaxed her grip on her temporary prisoner long enough for him to get a new grip on weapon in the split-second between him shooting her with his gun and her falling to the ground, knowing that she could never again regain consciousness in this body or this life.

_

* * *

_

Damn

... John thought to himself, shivering from a chill that had nothing to do with the temperature as he looked at Elizabeth's unconscious form, Sumner and Ronon lying a short distance away from her, one hand automatically adjusting his loosened mask so that it rested comfortably on his face once again. _That was _too _close_...

He knew that he should have thrown her off him as soon as she'd tried to pin him down, but even with the knowledge that it hadn't been _her _in control at the time, the feel of Elizabeth's body so close to his own... her smell... her hair... her hands...

He'd almost let his desire for what couldn't be take control of him, and come far too close to give Phoebus the chance to use him; he _couldn't _allow that to happen again.

Dammit, he'd already _accepted _that Elizabeth Weir didn't- _couldn't_- feel that way about him; how could he allow someone to use her body and try and exploit his desires like that? If she'd managed to pull it off, he'd have not only lost whatever trust he'd gained in Elizabeth's eyes over the past couple of years, but he would have lost every last _bit _of the self-respect he'd managed to hold on from the days before he'd become the Phantom.

Doing... _that_... with Elizabeth's body when she wasn't in control at the time...

_That _would have been crossing _way _too many lines for him.

Elizabeth and Atlantis might be safe now, but after what he'd almost done- and after what she'd _felt_; the feel of her fingers (Even if she hadn't been the one in control of them at the time) on what remained of his cheek had been a terrifying thrill, but it would attract too many questions-, he was _definitely _staying out of her way until he had to; maybe if he avoided direct contact with her for a while, she'd lose interest in asking about what Phoebus had felt under his mask...

It was a long shot, but he was going to give it a shot; _anything _was better than putting himself in a position where he would have to give Elizabeth such a clear look at what he'd become...

* * *

AN 2: Well, there you have it; the first teaser of what's actually _under _John's mask, and confirmation that it's not just there to make him look good yet intimidating.

Coming up next chapter, the introduction of a villain from the series who will have a VERY significant personal impact on John himself...


	17. A Fit of Jealous Rage

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This takes place after "Coup D'Etat" and a bit before the opening scenes of "Michael", so the Atlantis Expedition have only recently helped Ladon establish himself as leader of the Genii, and are currently experimenting with the retrovirus to transform the Wraith that will come to be known as Michael, although they've only gone so far as to acquire their test subject; Beckett's still testing the virus on live cell samples rather than injecting it into 'Mike' himself

AN 2: It's not my longest chapter, but I think it has its interesting points nevertheless; hope you like it.

Mystery of the Phantom

Standing on her usual balcony, Elizabeth once again wished that she knew what she'd done wrong; it seemed like the last couple of major missions that had been undertaken by the expedition had been far more morally ambiguous than she was comfortable with.

The situation with the Genii might have improved from what it had been before thanks to Ladon's apparent gratitude to them for saving his sister, but Elizabeth couldn't shake her apprehension about old examples of revolutions against dictators often ending up being just as bad as the government they were replacing; the fact that Ladon had been willing to go through with Cowan's plan until they had something to offer him left a part of her wondering what would happen if the day came when Ladon found something that he could take from them more easily than he could ask for it.

Of course, compared to the main project they were undertaking right now, an issue like diplomatic relations was quite frankly the least of Elizabeth's worries; her main concern right now was the current test of Carson's retrovirus.

She couldn't deny the obvious benefits of being able to remove the Wraith's need to feed on humans- particularly when it meant that they could eliminate the threat posed by the Wraith without having to actually _kill _anything-, but the ethical issues involved in the decision didn't make her feel particularly comfortable; however you dressed it up, she was essentially taking away another species' free will for her own benefit.

The Wraith might be killers, but they were killers because of what evolution had made them; even if it was to save lives, their current actions put Elizabeth in a moral quandary that she was far from comfortable with, and that was even before they knew if the retrovirus Beckett had developed was actually going to work...

Still... as much as those issues troubled her, the only real_ question _that had been plaguing her mind for the last few weeks was, as much as she hated to admit her selfishness even to herself, far more personal; her recent revelation about what John's face- or at least part of it- looked like under his mask.

She might not have Phoebus's first-hand experience of war zones or serious injuries, but she knew enough to be reasonably sure what bone felt like on her own, and what had been under John's mask, located approximately where his cheekbone would be, had definitely felt like bone to her fingers even if she hadn't been the one controlling them at the time.

She knew that John actually _had _skin, of course- what she'd seen on the exposed left cheek and around his eyes had confirmed that much to her satisfaction-, and she'd definitely felt flesh on the rest of his cheek, which meant that what she'd felt was some specifically-focused injury on that particular part of his face...

_So_, she mused to herself, _John wears that mask... because of an old injury_?

It made a certain sense, but it still didn't explain what kind of injury it was; what could have happened to John's face to make him feel like he had to wear that mask? Was it just out of a sense of personal vanity, or was there something more...?

"You're making a mistake," a voice said behind her.

For a moment, Elizabeth wondered if someone had found out about her association with the Phantom- it might not actually have endangered the city so far, but it wasn't like that would be enough to convince Sumner to leave it alone if he learned that she'd been secretly meeting with someone he was still suspicious about-, but then she recognised the voice and her fear was replaced by surprise.

"John?" she said, turning back to look at the man who'd just been dominating her thoughts, his cloak draped around his body in a manner that concealed almost everything underneath it apart from his feet, a cold stare in his eyes as he glared at her. "What are you-?"

"The Wraith in your doctor's lab," John said, glaring at her with an intensity she could only recall seeing directed at her when she was being held hostage by Kolya. "You _cannot _go through with the retrovirus experiment; it's a mistake."

Despite the fact that she'd been having her doubts about that very experiment only moments before, Elizabeth couldn't help but feel indignant.

"Excuse me?" she said, raising an eyebrow as she stepped forward to address the man before her, her arms folded as she glared at him. "Correct me if I'm wrong, John, but as grateful as I am for your help over the last year, you don't _actually _have any authority over what I decide to do in this city; the retrovirus is a legitimately-arranged experiment that gives us a chance to end this conflict bloodlessly by actually _helping _the Wraith get rid of their hunger-"

"I've been fighting the Wraith since before anyone on your planet even knew that the Goa'uld existed; I _think _that gives me the right to voice my opinion as an expert witness regarding this 'experiemnt'," John retorted with a firm glare, practically spitting his sentence out as he looked at her. "That... _thing_ in your isolation area is an _animal_, Elizabeth; even if there are a few Wraith out there who just eat to survive without taking any actual _pleasure _in it, I've never met a Wraith whose goals extended further than finding food supplies when they need them, and that kind of drive doesn't go away just because you change a few things."

"We'd be erasing his very _need _to feed-" Elizabeth began, hoping she sounded more resolved than she felt; John wasn't looking at the same arguments against the use of the retrovirus that she'd thought of, but that didn't make his points invalid.

"You can take out a lion's teeth, but that won't stop them _trying _to chew," John countered, an almost stone-like glare behind his mask as he glared at them. "He's been a monster for possibly _centuries_, Elizabeth; you're not going to get rid of that just by giving his DNA a tweak-"

"And what's the alternative, John?" Elizabeth asked, slamming her hand against the railing as she tried to stop herself giving into her doubts; she'd come too far in their research to turn back now. "Just keep on trying to blow up the Wraith on a hive-by-hive basis?"

"Why not; at least we can _guarantee _they won't hurt anybody again-!" John began.

"So you'd rather just kill them rather than give them a chance-?" Elizabeth tried to say, concealing the slight fear she felt at John's abrupt dismissal of the Wraith's right to live; they weren't perfect, but they were still living creatures essentially operating on instinct-

"THEY DON'T DESERVE A CHANCE!" John yelled, cutting off her train of thought as he suddenly reached out and grabbing Elizabeth by her shoulders, yanking her forward with such force that she found herself almost nose-to-nose with him in a manner that she'd never been before (She couldn't count how close-up they'd been when Phoebus was in control of her body as that hadn't been _her_).

For a moment, even with their current argument still practically filling the atmosphere around them, Elizabeth could only stare at the man before her, his eyes displaying anger mixed with a pain she couldn't quite place, the sudden shock of the scent of him- some combination of the sea and Atlantis and sweat and flesh and something uniquely _John_- filling her nostrils...

Then, as suddenly as it had been initiated, John's grip on her was released as he stepped back, his hands briefly shaking before he slipped them back under his cloak again, his gaze so cool that Elizabeth could almost believe nothing had happened if she couldn't still feel his fingers gripping her shoulders, the moment so unexpected that it felt as though he had taken hold of her on a level she'd never expected...

"I'm... I'm sorry," John said at last, his voice tainted with a bitterness that Elizabeth couldn't identify the reason for. "I just... I _can't_... they _don't_..."

Before Elizabeth could ask for John to elaborate on what he meant by that strange last comment, he had turned around leapt off the balcony, vanishing into whatever passage or location he used to return to the city when he did that before Elizabeth could even look over the balcony herself.

Elizabeth wasn't sure if it made her feel better or worse to know that John had the same doubts about the experiment as she did, even if he'd expressed in a more aggressive manner than she would have done herself...

But it was too late to start worrying about that now.

For all of John's talk about how they 'couldn't' use the retrovirus to 'rehabilitate' the Wraith, they'd progressed so far in their experiments with the virus that the expedition had to least attempt to use it; if they could turn the Wraith into humans, it could end the war in a matter of weeks by eliminating the very reason the Wraith wanted to kill in the first place.

If the alternative was just to kill every Wraith out there...

Elizabeth wasn't sure she could do that.

Actually, if she was honest, the fact that John _was _willing to do that...

It scared her a little.

Did whatever had happened to his face have anything to do with his vendetta- it was the only appropriate word- against the Wraith, or were the face and his anger at the species completely unrelated to each other?

* * *

_Damnit, damnit, DAMNIT_! John mentally berated himself as he crawled along the maintenance tunnels leading to his 'room' in Atlantis, cursing himself for the way he'd so abruptly lost control in those last few moments of his meeting with Elizabeth.

If only he'd given himself a chance to _think _about what he was doing, he might have been able to figure out a better way to phrase it... something that stopped him from showing all that emotion to the point where he'd almost lost control of himself...

God... if he'd _hurt_ Elizabeth, even only slightly...

He couldn't believe he'd done that... to _her_. It might just have been grabbing her shoulders- it wasn't even anything serious-, but still...

He just... _couldn't _let them use that retrovirus against the Wraith; they were nothing but animals who didn't _deserve _to be 'cured' of their condition after everything they'd done to the galaxy...

_No_.

He had to stop this.

He might have been able to bring himself to lie to Elizabeth for a few moments, but if he couldn't bring himself to lie about his motives to _her _for longer than a few minutes, he certainly couldn't keep on lying about his motives in his own head.

In the end, however, no matter how much John fought to deny it even to himself- he hated it when he admitted to something so selfish; it wasn't like he didn't _try _to be better than that-, there was only one reason he objected to the idea of the expedition using the Wraith retrovirus.

_Why them... and not me_?

What kind of a world was it that gave the creatures he'd dedicated his life to destroying a chance to become human after they'd caused centuries of suffering to this part of the universe... and yet left him in a position where his only way to survive was to become a monster almost as bad as they were?

How was it fair that the Wraith could just be given a 'clean slate' and have their sins 'wiped away' just because of some lucky break in genetic research, and he got left with nothing but memories and dreams of a life he'd once had and could never have again?

The retrovirus could give the Wraith a chance at a normal life... but what were the chances that _he'd _ever have that kind of opportunity himself?

Even if the accident hadn't happened, leaving him with no other option _but _to live like this, what he'd become as a person in order to survive this long...

In the end, all he was nowadays was a monster, no matter how much he tried to deny it; all he could do was ensure that, whatever he had become in his time in Pegasus, he continued to channel it in a manner that would help those who couldn't help themselves...

As far as the retrovirus went, with his attempt to talk to Elizabeth having failed, all he could really do right now was try to stay out of her way until he'd seen how the retrovirus experiment worked out.

If the retrovirus worked, he'd just accept it and hope that Elizabeth could forgive his 'rant'- although he'd need one _hell _of an apology if a chance occurred for them to meet before Atlantis experienced its next crisis-, and if it went wrong...

He'd be here to stop it.

He might be a monster himself, but he was a monster who would defend Atlantis- and Elizabeth Weir, of course- to the last; it was all he _could _do...

* * *

AN 3: Short, but it was mainly intended to set the scene; the next chapter starts during "Michael", featuring a confrontation between John and the infamous future Hybrid...


	18. Opposites

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Here we have it; shortly after 'Michael Kenmore' learns the truth about his Wraith origins, and his subsequent confrontation with the Phantom of Atlantis...

Mystery of the Phantom

As he sat in the quarters that had been 'his' since he woke up- he wondered if anything else had ever used these rooms and had moved out to better give them a 'lived-in' feel or if they had just given him somewhere new and hoped for the best-, Michael was left with little else to do but fume over the arrogance of what the expedition had done to him.

They had taken everything he had ever been from him in a carefully-planned of selfishness- he was only calling himself 'Michael' because he didn't know what _else _to call himself right now-, and they had the nerve to say that it had been 'for the best'? The only person who had definitively _benefited _from what they'd done to him had been _them_; they had clearly never even attempted to ask if he might _want _to go through with this... _experiment_...

They had judged him, sentenced him, and thrown away whoever he had been for nothing but their own gain; even if he couldn't remember anything about his life before he became human, what right did they have to assume that it was any better than the life he lived now?

For all their protestations that their actions had been for the benefit of others, they had killed _him _as thoroughly as if his body had died; the fact that he was still walking didn't change the fact that the person he had been was now gone...

"Trouble reconciling things, huh?" a voice said from behind Michael, apparently coming from his door.

"Actually," Michael began, turning around to address the speaker, "it's all pretty clear... to... me..."

His voice trailed off as he took in the sight of the man before him, dressed in a long black cloak and a silver mask that struck a chord in a part of Michael that he hadn't even been consciously aware of before this moment.

"_Phantom_..." he whispered, half-heard conversations he'd heard among the humans of Atlantis mingling with dim recollections of something he must have heard or learned about as a Wraith, stirrings in his subconscious mind that he couldn't entirely place leaving him with a deep sense of foreboding at being this close to the man with such a chilling reputation in this galaxy.

"Got it in one," the Phantom replied, nodding slightly at the other man before his eyes notably narrowed underneath his mask. "And, right now, we need to talk."

"About what?" Michael asked. "About how these humans you 'protect' from my kind-"

"_That _is what we have to talk about," the Phantom said, holding up a hand as he stared resolutely at the other man. "You are _not _one of 'your kind' now; you are _human_, and therefore entitled to my protection from the Wraith-"

"Oh, so now you're _blackmailing _me to stay human?" Michael spat.

"Blackmail?" the Phantom repeated, his expression through his mask as frustratingly unreadable as it ever was.

"You were going to say that you'd kill me if I became a Wraith again, weren't you?" Michael said, looking scathingly at the other man.

"Actually, I was going to point out that, in this case, protecting you just extends to convincing you not to become one again because of what it will do to _you_," the Phantom said, continuing to glare at Michael even as he neatly attempted to sidestep the question that he had just been asked. "If you become a Wraith again, you will be left with a near-constant hunger that is _never _going to stop, you will be driven to essentially eat other living creatures solely to sustain your own existence, you will lose virtually _any _ability to connect to other races-"

"And what makes you think I didn't like being what I was before?" Michael growled, still looking with disdain at his opponent. "You judged me because of what _you _perceived me as and that was it; you have no-"

"I wasn't involved in the decision to test the retrovirus," the Phantom interrupted, a slight wince on his face as though he regretted what he had just said passing as he continued. "Still, that doesn't change the facts of the situation here; you have a chance to be something _more _than what you were-"

"When nobody asked me if I _wanted _to be more than that," Michael spat back at his enemy. "They took everything I was from me because _they _didn't like it-"

"The expedition stopped you from needing to _kill _people in order to keep yourself alive and you're _complaining _about it?" the Phantom asked, his voice rising as he glared in increasing frustration at the other man. "Goddamnit, I'd have _killed _for a chance like what you had-"

"You would have _wanted _that chance; I never _asked _for this," Michael retorted, waving his arm at himself even as he privately noted that last comment for future reference; clearly, he was making more of an impression on his opponent in this little 'debate' of theirs than the other man might wish.

"They only wanted to _help_ you-!" the Phantom continued,

"You have the _nerve _to even _try _and imply that this was done out of _compassion_?" Michael spat. "They did it to me to make _their _lives better; nobody gave any thought to what _my _wishes were in this scenario-!"

"You weren't in a state to even consciously recognise that you might _need _help; you were the equivalent of a man who'd been blind all his life without ever realising that the possibility of seeing was an option-" the Phantom tried to interrupt.

"Oh, now _that _analogy is ridiculous; I wasn't _sick_-!" Michael interjected.

"You were sucking what you needed from others in order to sustain yourself because your body couldn't cope on its own; it might produce more drastic physical changes than a normal virus would have, but that sounds like a disease to me," the Phantom countered, looking in barely-restrained exasperation at the man in front of him. "You evolved to a point where you can't even exist independently on your own, and you actually think that's _natural_?"

"Who are you to say it isn't?" Michael retorted with a harsh glare. "Maybe the Wraith are _meant _to be the next step of evolution in this galaxy-"

* * *

"Don't even _try _that argument with me, _buddy_," John practically spat as he glared at the man he was already starting to think of as an opponent despite his best intentions when he came here; he'd tried to constantly remind himself that this man was, in a sense, just as much a victim of the Wraith as everyone they'd ever fed on, but it was hard to do it when he didn't even seem to _recognise_ the opportunity he'd been given. "Anyone who starts arguing that they're 'superior' to anyone else isn't going to win _any _points with me; your former race were parasites who feed on others because they can't cope on their own-"

"We're simply the top of the food chain around here, Phantom; it's _nature_," Michael interjected, cold resolution on his face as he stared at the other man. "We're stronger, faster, older-"

"And yet I've been killing Wraith for over a decade; you can't be _that _superior if _training _is all that we need to get the edge on you," John countered, trying to focus on creating

"You know what I've accomplished in this galaxy; doesn't the fact that I'm able to do that much damage to your people _by myself _prove that your argument about being a 'superior' life-form is a load of crap?"

For a moment, Michael just stared at him, a contemplative expression on his face that left John feeling uncomfortably like he might have just given away more than he should have done, before he broke the silence.

"You're not that different from me, are you?" the former Wraith said at last, a slight smile spreading across his lips as he spoke.

"What?" the Phantom asked, momentarily shaken before he glared at Michael. "Don't even _think _about that; I have _never _killed _anyone _who wasn't willing or able to kill me-"

"Oh, I'm not saying there haven't been occasions where you've let people live," Michael retorted, a slight smile on his face as he studied the other man. "And yet... you didn't become this because you _wanted _to, did you?"

"Don't go playing psychoanalyst with _me_, Michael; you don't know a _thing _about me-!" John growled.

"Oh, I know enough, Phantom," Michael retorted, a grim smirk as he studied the other man. "I know enough to know that you wouldn't choose a life like this- hiding in the shadows, striking and vanishing, never staying in one place long enough to get to know anyone as more than contacts- unless you _had _to..."

John tried to resist the temptation to reply- showing any kind of weakness to a _Wraith _went against everything he believed in-, but he was unable to completely suppress the shock and fear he felt as the man before him so precisely described how he felt about the life he had lived since that fateful day so many years ago, the life that necessity and duty had forced upon him to protect the city that had meant so much to the woman who had given his life meaning...

"Something _forced _you to become this..." Michael continued, contemplatively studying the man before him. "Just like _they_ forced me to become what I am now-"

"It's _not _the same," John spat, forcing down the rage he felt at this man's ability to almost automatically work out how he felt about his own past. "What happened to me was an accident that I had no choice but to adapt to; what happened to _you _is something that you could _accept_-"

"They _made _me something for their own convenience," Michael retorted, his hand waving at the window of his room that indicated the city. "I owe them _nothing_."

"You owe them your _humanity_-!" John protested; the idea that this man was being so blasé about having been given something that John would have practically given his eyes to have back again was _really _pushing him to his mental limits-

"I'm not _interested _in 'humanity'," Michael practically spat, a slight smirk spreading across his face as he looked at John. "I'm a Wraith, Phantom; humanity is what we _feed _on, not what we _are_."

For a moment, John could only stare at the man before him, his fingers clenching and unclenching as he fought down the urge to simply punch the man before him, forcing himself to recognise that anything he did in the way of physical attacks wouldn't help his case at this time, until he spoke once more.

"You don't _have _to do this..." he said at last, hoping that sheer desperation would help him where his attempted arguments hadn't. "You have a choice now; you don't _have _to be a Wraith..."

"But I _am _a Wraith, Phantom," Michael countered, a grim smirk on his face as he looked at the man in the mask. "Why should I be what others made of me?"

John could only stare back in frustration at the man in front of him, fighting to resist the urge to automatically try and continue the argument even as he found himself unable to think of another angle he could use to convince the man before him...

"You don't _have _to be a monster," he said at last, hoping that he'd managed to keep his voice steadier in reality than it had sounded in his own head.

"I've always been one, Phantom," Michael countered with a grim smile. "You can't change that."

And there it was.

Almost without knowing it- John had his suspicions that his previous 'arguments' might have given away his feelings on the topic, but he wouldn't like to swear to it-, Michael had isolated the main reason John had tried so hard to convince him.

Michael had been given a chance to become a man rather than a monster, and he'd refused it; it was almost as though he'd spent so long as a Wraith that he didn't even _want _to be anything else...

"Fine," he said at last, stepping back from Michael even as his gaze remained fixed on the former- and most likely future- Wraith in front of him, his expression the same neutral stare that had long stopped anyone recognising what he was thinking even when he was growing up all those long years ago. "But keep this in mind; if I meet you as a Wraith..."

"You'll kill me," Michael stated simply, before a sly smirk spread across his face. "Unless, of course, _I _kill _you _first..."

John didn't bother to respond to that; unlike everything else he'd experienced in this particular 'debate', straightforward death threats from his enemies were nothing unusual.

Turning towards the window of Michael's room, he opened the window and leapt out, his cloak spreading to slow the rate of his fall as he vanished from view into the depths of the city.

He wasn't too worried about the possibility of Michael seeing where he landed- the other man had too many things to think about right now to bother with seeing where a man he had no interest in talking to was going-, but even without that concern, two very prominent issues were currently occupying John's thoughts.

How long he would have to wait until the time came when he would need to fulfil the 'promise' he'd just made... and the implications of Michael's attitude towards his transformation on his own personal future.

If Michael had been so totally unwilling to even _try _and take the chance at humanity that the retrovirus experiment had given him, after living for so long as a Wraith...

Had he just rejected the idea out of disgust at being used as a guinea-pig without his consent- something that, in all fairness, John could somewhat understand; he'd just hoped that Michael would have seen the benefits of his new state more than the negatives-, or was it motivated by something... _deeper _than memory?

Had Michael been right when he said that you couldn't change once you became a monster?

* * *

AN 2: Not my longest, but another bit of personal analysis that I hope sets an interesting precedent for John and Michael's future confrontations in this series; next chapter looks at the events of "Inferno" (Events in the rest of the episode basically happened the same way as they did originally; Michael escaped from Atlantis and returned to his fellow Wraith as the retrovirus began to wear off), beginning with a _very _significant difference...


	19. A Trip to Taranis

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This begins a few days after Michael's escape from Atlantis, leading into the events of _Inferno_ (Albeit with some swiftly-obvious changes...).

Mystery of the Phantom

As Elizabeth sat solemnly at her desk, she wasn't sure what was worse; the fact that there was now at least one Wraith hive out there that knew about Atlantis's continued existence, or the fact that an experiment she'd already had doubts about when they'd started their research had gone so drastically wrong.

On a larger scale, the first was definitely the more problematic- even if for some reason Michael's system proved unable to cope with the transformation back to his Wraith self after so long as a human, there weren't that many viable candidates in this galaxy who had the necessary knowledge and resources to do something like that in the first place-, but it was the second factor that really troubled Elizabeth.

If the experiment had been a success, they could have at least justified their actions as helping to 'cure' the Wraith from a 'disease'- it wasn't hard to think of the Wraith as being 'sick', when taking into account that they ate normally when young; with that information you could almost consider them to be suffering from a deficiency that rendered them unable to produce enough of some kind of vital chemical to survive on their own after they reached a certain age-, but Michael's clear rejection of them for what had been done to him had reinforced Elizabeth's own initial misgivings about the whole project.

The retrovirus information might still be stored in their databases in case they found another use for it at some future date, but as far as Elizabeth was concerned their original plan for it would be nothing less than biological warfare releasing a weapon of mass destruction; the fact that the Wraith would still be alive afterwards didn't change the fact that who they were as _individuals _was gone...

The sound of the Stargate activating cut her bleak train of thought short, even before a glance at her watch confirmed that there were no offworld teams or contacts due to be getting in touch with them at this time; right now, any kind of offworld contact would be a welcome distraction from her current internal debate.

Getting to her feet, Elizabeth hurried over to the control room just as the wormhole connected to them, looking over at Chuck as he studied his screen.

"Anything?" she asked.

"Well..." Chuck said, looking at her with a slightly uncertain smile, "we _do _appear to be getting a radio signal of some kind; it's just not on any of our usual frequencies..."

"Radio?" Elizabeth repeated, looking at Chuck in surprise before she returned her attention to the wormhole before her. "Put the signal through."

"-_ellor Lycus of the Taranian Government for the city of Atlantis_," a voice said on the other end of the connection as the signal activated, the voice sounding like a man in his later years. "_Is anybody there_?"

For a moment, Elizabeth exchanged uncertain glances with the rest of the gateroom staff- evidently none of them had any idea who the 'Taranians' were any more than she did-, but in the end, she knew that there was only one way for her to learn anything else about this strange message.

"This is Doctor Elizabeth Weir," she said, after Chuck had activated their own radio. "I'm the leader of the Atlantis Expedition; who is this?"

"_I am Chancellor Lycus of Taranis_," the voice at the other end said, sounding slightly satisfied at this new turn of events. "_And, as I said, we have a message for those who now inhabit the city of the Ancestors_."

"And... who gave you this message?" Elizabeth asked.

"_The Phantom of the Ancestors, of course_," Chancellor Lycus replied, his tone shifting to something that made Elizabeth think of a combination of amusement and uncertainty; if she had to guess, she'd speculate that Lycus was testing to see if she was genuinely ignorant of who had told the Taranians to contact them or if she was just playing a joke of some sort.

"The Phantom?" Elizabeth repeated, a touch of apprehension in her chest at this latest news.

Even if she knew that the Phantom would never do anything to harm them- as she'd pointed out to Sumner more than once back in their early days in the city, it would be relatively easy for their masked resident to force them out of Atlantis if he'd wanted to make them leave-, she had a feeling that Sumner was going to examine anything that the Taranians had for them with the proverbial fine-toothed comb before he accepted whatever they had to offer.

"What... did he ask you to, exactly?" she asked, hoping that she'd managed to maintain the cool professionalism she'd worked so hard to create over her years as a diplomat (Introducing a personal element like John to negotiations always made her feel slightly less confident than normal, particularly given John's own... unique... nature, in terms of the difficulty in defining both his relationship with her- something she _really _didn't like to think about- and his relationship with Atlantis as a whole).

"_He simply provided us with crucial assistance in a... project... of ours, and asked that we pass it on to the people who would inhabit the city of the Ancestors in the near future_," Lycus replied, a slightly uncertain tone to his voice as he spoke; Elizabeth just hoped that their initial lack of recognition hadn't jeopardised their chance to gain a potential ally. "_We had heard... rumours... that the city was inhabited once again in the last year or so, but the Phantom's instructions were that we should only contact you when we required assistance, and to offer you the gift that he has assisted us in preparing for your use in exchange for your aid to us_."

"Assistance in what?" Elizabeth asked, even as she exchanged curious glances with some of the technicians in the gateroom; the implication that the Phantom had some connection with this society appeared to be a point of concern for some of the staff in the gateroom, but in general they seemed to be willing to listen to whatever Lycus had to tell them rather than automatically jumping to any negative conclusions.

"_On a personal level, we require assistance with some... technology... that we possess that is beyond our current technical understanding_," the man on the other end of the wormhole explained, sounding briefly embarrassed at the evident implications of that statement before he continued. "_On a wider scale, the Phantom's sole condition for providing us with assistance with a more long-term project- a project that I feel it would be best to discuss with you in person- was that we share our knowledge about the project with you when the time came for us to meet, and our people feel that now is as good a time as any for us to exchange information_."

"I... see," Elizabeth said, a moment of uncertainty crossing her face as she noted the uncertainty evident on the faces of the rest of her staff- clearly they were as unsure about the limited information as she was-, before she pushed that aside; John's motives might still be essentially a mystery to her, but she'd never been given a reason to doubt that he wanted to help. "We'll... be with you in a couple of hours; just give me time to assemble a team and we'll be there shortly."

"_Of course_," Lycus replied, his tone a professionally neutral one that Elizabeth had to admire; he sounded slightly disappointed that they weren't coming immediately, but it successfully avoided giving too much away about how he felt about this apparently unexpected response to his message (It was too bad that she wouldn't have the chance to talk with John about this turn of events; if it wasn't for the fact that he hadn't spoken to her since that whole mess with Michael, Elizabeth wouldn't have minded learning what his connection was with this society...).

* * *

"Is anyone else freaking out about the fact that this 'Phantom' guy apparently _knew _that someone would be coming to live in this city _apart _from him?" McKay asked, looking urgently at the rest of the people in the room as they sat around the conference table.

"Actually, the evidence that he _knew _anyone would be here is really pretty questionable," Elizabeth pointed out, even as she made a mental note to ask John how he'd known someone would come here herself (She vaguely recalled John once mentioning that he knew people would be coming to Atlantis, but she'd never managed to ask him for more about that bit of information). "All Governor Lycus said was that the Phantom requested that they share their discoveries with the inhabitants of Atlantis when his people needed assistance; it's perfectly possible that the Phantom intended to eventually use the city to provide refuge for other people in this galaxy, but we took control of the city before he could put that plan into action."

"It is... possible, certainly," Teyla admitted, nodding thoughtfully at Elizabeth. "The Phantom has been known to... provide those who have lost their homes with the address of other planets where they could live in the past; it may be that he was intending to establish a residence for those that he felt could be trusted with the secrets of the Ancestors in this city itself..."

"Well, they're not here and we are," Ronon said with a slight shrug as he looked around the table. "Sucks for him if we disrupted any plans he had going on, but as it is, we're here and nobody else is; if they've got something that can help us, I say we just go and get it."

"Not exactly the best way to phrase things, Ronon," Sumner said, looking pointedly at the Satedean before he turned his attention back to Elizabeth. "Still, phrasing aside, he makes a point; if these people are willing to share some of their recent discoveries with us, I don't think we have any particular reason to reject their offer."

As much as Elizabeth couldn't help but find this decision somewhat ethically questionable- they might not exactly be lying, but the evidence available to them did suggest that John might have been planning to give the Taranians' as-yet-unknown research to somebody else-, she couldn't shake the fact that Ronon and Sumner had made valid points; no matter who John had _intended _to bring to Atlantis, they were the ones who had taken up residence in the city in the end.

The memory of her old argument with Sumner about how the Phantom could have driven them out of the city himself if he hadn't wanted them there briefly came to mind, but they didn't make her feel entirely comfortable. When she'd made that argument, a part of her had assumed that John knew significantly more about Atlantis than they did; her conversations with him over the last few months had suggested that his experience with the city wasn't as extensive as she'd first believed, which created the idea that he'd only accepted them being there because he _had _to...

Still, no matter what doubts Elizabeth might be feeling now about the situation facing her, that didn't change the facts; if John had thought that something was worth working on, that it was probably something interesting.

"All right," she said, nodding at her team. "Just... remember not to do anything that gives away the fact that we don't actually _know _the Phantom personally, and we should be all right."

"Please, we're _masters _of discretion," McKay said with a reassuringly smile. "Trust me; they won't get _anything _to suggest that our social circle doesn't include the Phantom."

* * *

As Sumner looked out from the windows of the former Ancient facility that the Taranians had used as a base for some time, he had to admit that he was at least slightly impressed. The facility might have seemed more like something he'd see on Earth than an Ancient construction, but it still made for an impressive display by the usual standards of architecture seen in Pegasus so far, and the apparent depth of the tunnels inside the mountain was also impressive by any definition.

As for the Taranians themselves, while their knowledge of the technology they were dealing with wasn't precisely as advanced as the Atlantis expedition's own, Sumner had to admit that the expedition had the slight advantage of having developed various examples of computer technology on their own; as with most of the more advanced species in the Pegasus Galaxy, the Taranians had been forced to develop in secret in order to create most of their technology, and even then most of what they had developed more recently was apparently based on what they'd gained from the Phantom.

Still, even with the more 'primitive'- by Ancient standards, anyway- technology in the base compared to the resources the expedition had discovered in Atlantis, the Taranaians seemed to have progressed well. Aside from their ability to maintain any kind of Ancient structure with at least some degree of understanding of its original purpose, Sumner had even noted some examples of what looked like primitive stun weapons on the holsters of some of the members of the facility's security force that they'd encountered earlier, most likely based on information recovered from the databanks, although the weapons were obviously bulkier than most true examples of Ancient technology that they'd encountered.

"So, you've been using this facility's shield to protect yourself from the Wraith?" McKay asked, looking curiously at Noreno Pero, the woman who had been introduced to them as the Taranian's chief scientist (Although Sumner privately had to wonder how much of that was because he believed her tales of her expertise or because she was just attractive; if he'd been a bit less professional, Sumner had to admit that he might have been tempted himself).

"Yes, we discovered it some decades ago after our use of a series of underground caverns lead us into this facility," Norena explained, smiling slightly at McKay as she spoke. "What knowledge we've gathered about it on our own is rudimentary at best, but the Phantom's assistance allowed us to develop a better understanding of what we were dealing with; he was even able to provide us with the facility's instruction manuals, including that it's powered by geothermal energy from the volcano beneath us, although our mutually limited knowledge of their language has meant that we've only been able to progress so far."

"Oh, it's a translation issue?" McKay said, smiling at Norena before a warning glare from Sumner- they had to ensure that they maintained the idea that they were at least casual acquaintances of the Phantom in order to find out what the Taranians had discovered- prompted his smile to dim slightly. "Well, we've picked up a bit more about the language since... the Phantom last saw you; we might be able to find out a bit more about what the problem is."

"You said that this place is run by geothermal energy?" Sumner asked, looking over at Lycus- the man's suit might be old, but it was at least more professional than Norena's slim purple dress- as McKay and Norena turned to begin their analysis of the control console that had been identified as the shield generator, Ronon following the Canadian after a brief nod from the colonel. Teyla was staying with Sumner as the team's unofficial diplomat, but the Satedean's presence might be useful in making sure that McKay stuck to the story; Ronon's tact might be questionable at times, but he was as interested in securing a potential weapon against the Wraith as Sumner was, and that was the main thing right now.

"From what my scientists tell me, at any rate; what I know about the shield's operating systems personally is limited," Lycus said, only a slight trace of discomfort on his face at this admission.

"I'm pretty much the same when it comes to what we use back in Atlantis," Sumner replied with a slight smile of understanding; in a situation like this, it didn't hurt to establish common ground with another leader. "We all know our strengths, and that's the important thing."

"Quite," Lycus said, relaxing slightly as he turned to indicate another door. "In the meantime, while our scientists begin their work, perhaps you would care for a tour of our facility?"

"Lead on," Sumner replied with a nod.

With that consent, Lycus lead Sumner and Teyla into an elevator at the back of the room that bore a slight resemblance to the teleporters they used in Atlantis. The subsequent descent brought them to a deep storage area that put Sumner in mind of some of Atlantis's more distant storage areas.

"My ears just popped," Sumner noted as he, Teyla, and Lycus's group left the elevator, unable to stop himself making the observation despite his attempts to maintain authority; he'd known this place was deep, but he hadn't expected it to be _that _deep...

"We are deep underground," Lycus clarified. "The Ancestors constructed an extensive system of corridors and tunnels throughout the facility and beyond."

"Like the one that lead you to discover this facility originally?" Teyla asked.

"Precisely," Lycus confirmed, as he and his men continued to walk through the facility. As his ears adjusted to the new pressure, Sumner noted that, while the base looked similar to Atlantis in terms of interior design, the addition of what looked like pressure valves and pipes made Sumner more inclined to think of a submarine rather than a grounded base (He wondered if this facility had once been capable of motion before it was buried here for some reason)-

A sudden brief but violent tremor shook the entire base, nearly sending Sumner staggering into a nearby set of pipes before he regained his balance just as it ceased; he wasn't sure if he should be more perturbed at the slight loss of dignity or the fact that Lycus appeared to be totally unperturbed by the incident.

"What was that?" Teyla asked anxiously.

"Oh, just a tremor; nothing to be concerned with." Lycus said, a dismissive smile on his face as he turned to look at Sumner. "Please, this way."

Sumner was grateful that Teyla looked as uncertain about the chancellor's casual dismissal of the tremor as he was; he wasn't exactly wild about earthquakes on any scale even when he _wasn't _underground, and the concept that people who spent most of their time in an underground base would be that dismissive about the potential dangers of such an occurrence...

"This is the main hangar," the chancellor explained as he paused in front of a large door.

"Hangar for what?" Sumner asked, thoughts of earthquake-related dangers momentarily pushed aside in favour of this possible new addition to their still-developing picture of the Taranians.

"Our collaborative project with the Phantom," Lycus clarified, a slight smile on his face as he waved his hand against a standard Ancient door panel. "I assure you, mere description is inadequate."

As the door opened, Sumner couldn't stop his jaw dropping at the sight that greeted him.

The size of the room before them alone would have been impressive- he could think of quite a few buildings from Earth that could have been comfortably placed inside this area, and the fact that it was underground made the engineering that must have gone into its construction all the more impressive-, but the most striking detail about the room was what it contained.

There, on the ground below the balcony where they currently stood, significantly larger than even the _Daedalus_, was a vast ship that Sumner quickly identified as Ancient design, resembling a more intact and slightly larger version of the _Aurora _that Atlantis had briefly encountered a few months ago.

"I see what you mean..." was all that Sumner could say at the sight.

"The Phantom called it the _Orion_," Lycus said, looking at them with a slight smile (Sumner noted the anomaly of the name, but preferred to focus on the chancellor's explanation right now; he'd consider further implications later). "We have managed to piece together most of the essential power connections, but some particular pieces of hardware still need some work; we're hampered by such factors as our inability to determine what is actually required for us to complete the work..."

"And... you believe that we will be able to assist you?" Teyla asked.

"The Phantom requested that we provide the Atlantis Expeidition with whatever resources we could to assist you in your struggle against the Wraith," Lycus clarified, indicating the ship before them with a slight smile. "We do not have the resources to completely repair or use the ship effectively ourselves- he mentioned a particular... gene sequence, I believe was the term used... that is necessary for people to successfully operate the technology of the Ancestors-, but if the Phantom believed that you could assist us in completing what we began when repairing it, I feel that we can afford to trust you."

Sumner wasn't sure what shocked him more at this point; the sheer scale of the discovery they'd just made, or the ease with which Chancellor Lycus was willing to share it with them based only on the Phantom's word.

"You... have a great deal of respect for him, don't you?" Sumner said at last.

"He assisted us in learning a great deal about the technology available to us; after everything that he has done for us, and the galaxy as a whole, it would be foolish _not _to be grateful to him," Lycus replied, shrugging slightly as he looked back at Sumner. "Why do you ask?"

"Oh, it's nothing personal; just... had a couple of past alliances that didn't work out as well as we could have liked; I like to get a good first-hand perspective on everyone's motives," Sumner clarified, hoping that Lycus didn't take offence at the near-miss before he indicated the ship below them, hoping that a little improvisation would cover up how close Lycus had come to touching upon the ever-awkward topic of his own thoughts about the Phantom. "In any case, from what we can see, it looks like... reports of your progress were accurate; from what I can see things seem to be in good shape."

"Yes, with the plans provided by the Phantom we have managed to re-connect most of the crucial systems together, although some of the fine details regarding the actual hardware- or, according to our scientists, the programming that controls it- has so far proven beyond our ability to completely repair it," Lycus said, his expression shifting to become slightly curious as he looked at Sumner. "I acknowledge that my people would obviously prefer for the shield to be repaired first, but if he would be willing to take a look..."

"Of course," Sumner said, nodding in resolute confirmation. "I assure you, once Doctor McKay's finished analysing your shield, he will be perfectly willing to provide his assessment of your progress with the... _Orion_... so far."

Even though he knew that McKay would unquestionably be willing and interested in volunteering his services in repairing the ship before them, Sumner couldn't help but feel slightly uneasy about the current deception- no matter how minor- regarding his connection to the Phantom.

He might stop not entirely trust that the man's independent attitude wouldn't put the city in danger at some point in the future- his continued insistence at doing things his way rather than being answerable to any kind of higher authority was going to cause a problem at _some _point, Sumner was sure of that-, but he did appreciate that the man's skills and experience had saved Atlantis more than once in the past; not liking someone didn't mean that he had to dislike the man's accomplishments.

He might not be entirely comfortable with Lycus's near-reverential attitude towards the Phantom, but he also couldn't deny that the man had picked up an obvious reputation among the inhabitants of the Pegasus Galaxy, which he definitely _hadn't _acquired by failing in his apparently self-appointed mission...

In the end, the thing that occupied his mind most right now- he'd leave the issue of whether they could get the ship working or not up to McKay- was the issue of the ship's name.

_Orion _might be an interesting name that he saw no reason to change, but that didn't alter the fact that it was a name from Earth mythology that had no place being used by someone in _this _galaxy...


	20. Volcanic Panic

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This picks up shortly after the last chapter ended; Elizabeth has been briefed on Sumner and McKay's discoveries so far and has come over to talk about the possibility of the Atlantis expedition using the _Orion_

Mystery of the Phantom

As she sat in Chancellor Lycus's office on the other side of his desk, Elizabeth couldn't help but be grateful that Sumner had agreed to allow her to handle this herself; at least this way she could use her friendship with John to help her make a case for the Taranians to allow Atlantis to examine the _Orion _without worrying about revealing things she wasn't ready for the rest of the expedition to know.

On an encouraging note, based on Sumner and Teyla's own analysis of the ship so far- along with what little attention McKay had been able to give it in between his research into the shield-, apart from the subspace beacon that had allowed them to detect the _Aurora _being virtually shattered on this ship, the _Orion _seemed to be in relatively good condition. While whatever had happened to put it in this position had resulted in the programming codes controlling the ship's ability to fly anywhere being almost completely wiped, along with some damage to particular crystals in the main computer, Atlantis still had records of the necessary programs in its database even before their encounter with the _Aurora _last year, and the plans they had acquired while investigating the ship in question should allow them to determine how to replace the missing crystals...

"So," Lycus said, drawing Elizabeth's attention back to the present as she focused her attention back on him, "you believe that your city's knowledge has progressed sufficiently since the Phantom last came to us to complete the work that we have started?"

"Only because we had a lucky break a few months back when we discovered a previously-unknown... relic of the Ancestors... with more information about their ships than we had previously possessed," Elizabeth said; she didn't think it would entirely help their case if Lycus knew that they'd already destroyed one Ancient ship after salvaging it, even if the ship had already been almost irreparably damaged before they'd found it.

"I see," Lycus said, nodding slightly at her in understanding, an expression of silent contemplation on his face for a few moments before he smiled slightly at her. "Well, if the Phantom believed that you were worthy to learn the secrets of the city of the Ancestors with him, I feel safe in trusting you with our own discoveries."

"Thank you," Elizabeth replied, nodding back at him in gratitude. "I'll be sure to let you know what we find... once Doctor McKay has finished his analysis of your shield generator, of course; we fully understand that it's your main priority right now."

"Yes, we've used it to help protect many others from the Wraith-" Lycus began.

"_Sumner to Weir_," a voice suddenly said in Elizabeth's radio.

"Excuse me, Chancellor," Elizabeth replied, looking apologetically at the older man before she activated her radio. "Yes?"

"_McKay's just discovered a problem with the Taranian's shield generator_," Sumner replied, his tone grim as he spoke. "_You'd better get down here now_."

"We're on our way," Elizabeth said, standing up and looking apologetically at the chancellor. "You should probably come with me; I just received a report from Colonel Sumner, and apparently Doctor McKay's discovered that something's wrong with your shield generator."

"The generator?" Lycus repeated, apprehension clear on his face as he stood up and walked after her as she headed towards the lab. Even without her long experience of McKay's moods, Elizabeth would have quickly seen that the Canadian scientist was concerned about the latest turn of events; his expression displayed an apprehension that he'd only previously shown when they were waiting for the Wraith to reach Atlantis.

"What's wrong?" she asked, hoping that Lycus wouldn't take offence at her taking control of the current inquiry; since it was someone on her team who found whatever had just been discovered, she felt a certain responsibility to establish the current crisis.

"Well," McKay said, turning to face her as he spoke, "as we were all already aware, this facility is powered by geothermal energy- which exists in this area in sufficient quantities to supplant the traditional need for a ZedPM that would normally be required for a facility like this-, and it's been experiencing various harmonic tremors in recent months."

"Which means?" Ronon asked.

"_So_," McKay continued, "according to Norena, the tremors began when she was forced to make some modifications to the system to compensate for recent fluctuations in shield strength, _after _they turned the shield on and have since kept it running for the better part of a year in response to the sudden rise in Wraith activity that began last year..."

Elizabeth wasn't sure if she should be grateful or not for the fact that she wasn't a swearer by nature; it might have given the game away if she'd said anything at this point, but there were times when news like that made her want to vent her frustrations with a simple curse word or two...

"And I assume that this shield wasn't designed to stay on like that?" Sumner asked.

"Bingo!" McKay confirmed, pointing in confirmation at Sumner before he lowered his finger as the colonel glared at him in a very pointed manner for his lack of professionalism.

"Uh... anyway," the Canadian continued, quickly overcoming his momentary discomfort as he looked at the people around him, "the _problem _is that this facility was never designed to be continually run at maximum capacity. It was a good idea based on what you _knew _of the situation, don't get me wrong, but shields are intended for emergency uses only; when you shut down those alarms you mentioned earlier, you overrode the failsafes which stopped them..."

His voice trailed off as he studied the information now on display on his laptop, his eyes widening in horror. "Oh no..."

"What?" Norena asked, looking inquiringly at McKay as she and Sumner walked over to study the laptop with him.

"The reason the Ancients chose to power this facility on geothermal energy is because we're sitting right smack in the caldera of a dormant supervolcano," McKay clarified, looking grimly up at his team leader and the attractive Taranian scientist. "Or should I say, _formerly_ dormant, because drawing all of this energy from the magma chamber has made it extremely _active_."

"And that means that things are about to get worse, right?" Sumner asked, raising an eyebrow at his team's scientist.

"To say the least," McKay replied, nodding pointedly at the other man.

"Hold on a minute; you said we're _inside_ a volcano?" Elizabeth asked, trying to regain some kind of control of the current conversation as she walked over to a nearby window. "I don't see anything like that..."

"Because you're standing _right inside _it," McKay said, steepling his fingers to create a traditional triangular volcano-shape. "Look, when you think a regular volcano, you think Mount St. Helens or, uh, Kilauea."

"And... supervolcano?" Elizabeth asked apprehensively.

"Yellowstone National Park, with a caldera over fifty miles wide and a massive sea of molten rock just beneath the surface," McKay clarified.

"So, the Ancients built this facility to draw on geothermal energy because it had access to all that power?" Sumner asked, looking over inquiringly at McKay before he turned to study the view outside the window thoughtfully. "I'm guessing these 'supervolcanoes' don't erupt very often?"

"Yeah, normally, thousands, often _hundreds _of thousands of years can go by before these things go off, but unfortunately these... well, they aren't normal circumstances," McKay said, looking awkwardly over at Norena as he continued to speak. "It's nobody's fault- there's nothing in the plans that actually _said _this would happen, after all; the Ancients never exactly predicted that _anyone_ would do what you've been doing-, but by drawing on the geothermal energy continuously for the last year or so, you've increased the pressure of the magma chamber; it's expanded to over forty miles now, and it's _still _increasing."

"Can it be stopped?" Elizabeth asked, her mind struggling to comprehend the scale of what McKay had just told them; if they were currently _inside _a volcano, judging by what she'd seen of the area outside this facility when she'd come through the Stargate, the potential power of the eruption would be _incredible_...

"No; the damage is already done," McKay said grimly. "Look, a significant hotspot rift has opened. The pressure will keep building as magma continues pouring in directly beneath us."

"Could we relieve the pressure by providing the magma with somewhere else to go?" Sumner asked. "We could launch a drone into the crust at the other side-"

"Not _everything _can be solved with military force, Colonel!" McKay said, glaring at Sumner in exasperation. "When this thing goes, the _whole _thing goes!"

"Right..." Sumner said, before he turned to look resolutely at Lycus. "We need to evacuate your people; we can help you establish a suitable alternative location on this planet if you don't have one already-"

"Look, you're _still _not getting it!" McKay yelled, looking in exasperation at his team leader. "Listen to me, _all _of you; when this thing erupts, the force of the explosion will be over ten thousand times greater than the blast that destroyed Mount St Helens. It will obliterate half of this continent!"

"There must be other continents-" Elizabeth began.

"The dust cloud will envelop the planet within weeks, blocking out enough sunlight to kill every living thing; we are talking about an Extinction Level Event!" McKay yelled, before he turned to address Lycus in exasperation. "Look, the only option you've got is to evacuate your people to another planet, and I would advise doing it sooner rather than later."

For a moment there was silence as Lycus looked contemplatively at McKay, before he turned to face Elizabeth.

"You are all certain of this?" he asked.

"Chancellor Lycus, Doctor McKay is the finest scientist we have," Elizabeth said; as much as she hated confirming McKay's ego at a time like this, she didn't have a choice when this many lives were at stake. "I trust his advice without reservation-"

"And I acknowledge that the Phantom has proven time and again that he would not trust anyone with guardianship of his city unless he was certain that they could be trusted," Lycus said, looking grimly at her for a few moments before he nodded in a reflecting manner. "While the timing of this eruption is... unlikely, I cannot deny that the tremors have become increasingly more prevalent in the last few weeks since I ordered that we maintain the shield on a regular basis, and I can foresee no way for these incidents to be the fault of another."

Elizabeth said nothing as Lycus stared out of the window at the vast volcanic expanse around them- even McKay remained silent, evidently recognising that anything he said right now was more likely to be the wrong thing to say-, until he nodded in resolution.

"Norena," he said, turning to look at the Taranian scientist, "tell our people to gather their most precious possessions and prepare for evacuation through the Ancestor's Ring; we must find a new planet-"

"You can evacuate to Atlantis for the moment," Elizabeth added; hopefully the offer would improve the chances that Lycus would accept their offer without asking too many questions about the Phantom. "We can work on finding something more suited to your individual survival later, but if we can't help you sort out your shield problem, we can at least give you somewhere to stay in the short term."

"Thank you," Lycus said, nodding back at her.

"Talking of evacuation plans," McKay said, looking hopefully around at his teammates and the Taranians, "if we move some people into the _Orion_, I'm _fairly _sure that we can use that to help us evacuate some of the population-"

"I thought you said that the _Orion _wasn't operational yet?" Sumner interjected, looking pointedly at McKay.

"Well, not _yet_, but it's not that far off; everything's connected up properly, but the main problem is that most of the crystals containing the necessary programming code to activate the propulsion systems have been damaged and nobody here knew the programming codes necessary to use the back-up crystals as replacements," McKay explained with a noticeably more enthusiastic smile. "I've still got the information we recovered from _Aurora _and Atlantis's databanks; give me a couple of hours to make sure I know what needs replaced-"

"Do we have that time?" Sumner interjected, staring pointedly at the scientist.

"Uh... well, we _should_; the magma build-up's inevitable, but it's not going to be _immediate_, so we should still have _some _time if I'm quick..." McKay said, momentarily hesitant in the face of Sumner's stare before he straightened his stance in resolution and turned around to hurry towards the hanger where the _Orion _was stored.

After Elizabeth had exchanged glances with her military commander, she shrugged slightly and turned back to look at Chancellor Lycus.

"I apologise for Doctor McKay's... abrupt departure... but he makes a valid point," she said, hoping that Lycus didn't object too much to her issuing this many suggestions so soon after their first meeting; she might have more experience in this kind of situation than him, but she also recognised that he didn't become leader of his people for nothing. "Whatever else happens right now, our best chance for saving as many of your people as possible is getting them through the Stargate or McKay completing the repairs to the _Orion _that you've already started; I assume that you have some idea of how many people it could hold if you had to use it?"

"Yes, we've measured its interior and it's always been able to hold a significant portion of the refugees we have staying with us at present; as you said, we felt that it would have a good secondary refuge if we were able to get it working again," Lycus replied.

"Good," Elizabeth said, smiling at him in thanks before she became more serious. "Let's go; we don't know how long we'll have, so it's best to get started."

* * *

As Sumner stood at the Taranian DHD, Teyla and Ronon coordinating the evacuees towards the Stargate while McKay went over the available information on the _Orion_ and the newly-arrived Doctor Beckett checked out any injured, he wondered how things had come to this; they find what could be the second most exceptional remnant of the Ancients' legacy left in this galaxy- the Tower of the 'Lord Protector' didn't count as it was in such bad condition there had been virtually nothing useful left of it, but _Orion _seemed to be in significantly better shape-, and they barely have time to _start _looking at it before they had to work on evacuating an entire civilisation...

It was a relief that most Taranians lived near the facility; at least it meant that they didn't have to worry about sending out messages to the more distant territories that would probably never get there in time to make a difference. Doctor Weir and Chancellor Lycus were already preparing to travel back to Atlantis with the first batch of refugees, and his last report from Teyla had assured him that the rest of the Taranians were making excellent progress preparing for their departure.

"Sumner to Weir," he said, as he finished entering Atlantis's address into the dialling device. "The Stargate's been dialled; you're good to go."

"_Acknowledged_," Doctor Weir's voice said on the other end of the line. "_See you back in Atlantis_."

As Sumner watched the Stargate through the window in front of him, Doctor Weir and the Chancellor advanced through the now-active wormhole in the middle of the stone platform, closely followed by the first collection of Taranians assigned to the evacuation plan.

As the refugees departed, he allowed himself a few moments to relax; he might prefer the missions where his team won a victory over the Wraith, but there was still something satisfying in helping people escape this kind of danger...

Then a violent earthquake shook the complex, triggering a burst of steam from the ground immediately in front of the Stargate, and Sumner was motivated into action even before the large circle that had changed and affected so many lives across so many planets began to sink.

"Ronon, Teyla; get those people back inside immediately!" he yelled, thought quickly translating into action as he activated his radio to alert the rest of his team before he changed the setting once again. "Sumner to Atlantis, raise the shield; the Stargate is sinking into the magma!"

As he watched the sight in front of him, the refugees retreating as the stone platform began to collapse in bursts of molten orange, all Sumner could do was watch helplessly as the Stargate fell over onto its front and began to sink into the ever-expanding pool of lava surrounding it.

For a few moments, all that Sumner could do was stare at the sight of the area where the Stargate had been only moments before; he knew that the Stargate could survive almost anything thrown at it short of the 'Gatebusters' he'd heard rumours of during his trip back to Earth, but the scale of what had just happened... coupled with the sheer random bad luck of it...

"What happened?" Ronon asked, as he, Teyla and Beckett hurried into the control room, their arrival drawing Sumner's thoughts out of the momentary panic that had been about to set in; he had a situation facing him, and he had to present a controlled front for the rest of his team if they were going to get through this.

"The Stargate sank into the magma just after Doctor Weir and Chancellor Lycus passed through with the first wave of refugees," Sumner clarified, looking grimly back at his colleagues.

"What?" Beckett asked, looking in shock at the colonel before his gaze returned to the expanding magma before them. "Oh God... we are in _serious _trouble..."

"Maybe not," Ronon said, looking over at Sumner with a thoughtful expression. "The Taranians have said a bit about that ship of theirs in the hanger; maybe McKay could finish the job."

For a moment, Sumner wondered if that idea was even possible- he knew that the _Orion_ was in relatively good shape, but even with whatever advice the Phantom had been able to provide he doubted that they could have _completely _put the ship back together given their own pre-existing technological development-, but pushed that thought aside; with no immediate way to contact Atlantis, and no way of knowing when the _Daedalus_ would get here- assuming that Doctor Weir was able to reach Colonel Caldwell in time to make a difference-, that particular plan most likely represented their greatest chance of survival using the resources available to them.

"It's... worth a try," he said at last, nodding briefly at Ronon in acknowledgement of the Satedean's suggestion before he turned to Teyla. "See what you can do about coordinating the remaining refugees; I'll check in with McKay and see how things are going at his end."

It wasn't much of a plan, but it was probably the best that they were going to come up with in the time available to them; Sumner just hoped that McKay's usual brilliance when faced with something that would kill him if he screwed up remained valid...


	21. Launching the Orion

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Like the last chapter, this takes place shortly after the previous one; McKay's just been filled in on recent developments and is continuing his analysis of the _Orion_ based on Ronon and Sumner's latest suggestion

Mystery of the Phantom

"OK," McKay said, his concentration focused on the console in front of him, praying that what he recalled from his time on the _Aurora_ was accurate- working the computers was one thing, but turning them on was something else; from what Norena had told him the Phantom's instructions had mainly focused on completing the physical repairs for the ship rather than analysing the condition its operating system was in- as he prepared to attempt activation of the ship's systems. "And primary power... is... online."

Much to his relief, the console activated, followed by the rest of the consoles in the ship's bridge quickly turning on afterwards; clearly the Taranians had done a good job in terms of physically repairing the damaged components even if they hadn't been able to turn much of the ship on afterwards.

"I wonder how many more ships like these exist," Teyla mused.

"A few more like this, and we can give the Wraith a serious fight," Ronon commented, a slightly approving smile on his face.

"Life support should be back up and running in a few minutes," McKay added as he walked around the control room, briefly checking a few consoles before he turned to address the others.

"Good work," Sumner noted briefly, nodding in approval at the Canadian; he thought about asking why life support needed to be reactivated in the first place, but reminded himself before he even spoke that it probably wouldn't have been considered a necessity to keep life support on when so many other systems needed work and the ship was on the ground anyway.

"And I've discovered the ship's name- its _original _name before the Phantom named it, I mean," McKay added, glancing briefly at his portable computer. "It's named the, uh-"

"_Hippoforalkus_," Norena added, smiling slightly at him.

"Huh?" McKay said, looking at her in surprise. "You know that?"

"Yes, the Phantom discovered that when we first managed to activate the ship's computer systems; we left it off more of the time as we did not want to drain the ship's power, particularly since we were unable to do much about damage that the operating systems had sustained without access to the programming codes to do so, but a casual analysis allowed us to better determine what hardware was in functional condition and what was not," Norena clarified, smiling slightly as she looked around at the rest of the team. "The Phantom felt that 'Orion' was a simpler name for all concerned, and we agreed with him after he provided us with the tale of the original Orion; a mythical hunter whose skills attracted the attention of his world's gods seemed a more appropriate name for such a ship than a general that we knew nothing about."

"I... see," Sumner noted, wishing that he could work out whether that particular piece of information was relevant to his efforts to find out more about the Phantom or not; could it just be a coincidence that the Phantom came from a world that shared at least that myth with Earth, or was there more to it than that?

"Whatever its name," Teyla said, drawing Sumner's focus onto the presently most relevant issue, "this ship is large enough to fit many people."

"Could fit all the settlement if we had to," Ronon added.

Sumner was trying to decide how he felt about that idea, but the sound of his radio activating drew his attention in another direction.

"_Colonel Sumner, this is the _Daedalus," the voice on the other end of the connection said.

"Go ahead," Sumner replied as he turned his radio on, only to wince as nothing but static reached his ears.

"We're too far underground for conventional signals to reach us..." he muttered, half to himself, before he turned to look at McKay. "Can you get this ship's communications systems online?"

"Right, I'm on it," McKay said, hurrying past Sumner to another console and activating a few controls. "Right, try it now."

Nodding briefly in response, Sumner activated his radio. "We're here, Colonel Caldwell; what's your status?"

"_We've just arrived in orbit above Taranis_," Caldwell clarified. "_Where are you? We've scanned the base and found no life signs_."

"Well, this part of the complex must be, uh, shielded," McKay suggested as Sumner looked inquiringly at him.

"_I hear you could use some assistance_?" Caldwell said.

"Quite," Sumner confirmed with a grim nod. "The Stargate on this planet has been swallowed by lava and the volcano we're in is about to erupt within the next few hours; any assistance that you can provide would be appreciated."

"_Get yourselves out into the open where we can get a lock on you_," Caldwell responded.

"That's not going to be possible," Sumner replied; as much as he prided himself on his rationality, he knew that this was one occasion where he had to at least _try _and save everyone involved in this current mess. "We're working on evacuating the population, and we've managed to locate an Ancient ship that these people have mostly repaired that we can use for that purpose, but Doctor McKay's still working on making sure everything's connected up properly; right now, the most useful thing you could do for us is get some of these people back to Atlantis so we don't have to worry about them ourselves."

"_Just to clarify, you don't expect us to take _everyone _on that planet, right_?" Caldwell asked. "_From the number of people we're detecting, that would be at least four trips_."

"_Daedalus _is quite large," Teyla put in. "Sure you could fit more..."

"_This __is a spaceship, which means that our life support resources are finite_," Caldwell interjected. "_Four trips would already stretch those resources to the limit_."

"Just give me a minute, and I'll get back to you on that," Sumner said, before he terminated the connection- it might be rude, but this was something it would be best to discuss with his team before he told anything to the other colonel- and turned to McKay. "How long would it take to get this thing ready to fly if we focused on propulsion and ignored weapons for the moment?"

"Well," McKay said, studying another console contemplatively, "actually, most of the power regulators are up and running, the connections are all sorted, even the hyperdrive seems to be ready to go; the only thing _not _operational right now is..."

He paused for a moment before he groaned in frustration. "Oh, _crap_."

"Problem?" Ronon asked.

"The one system that's in _really _bad shape, and it's the sublight engines," McKay said, looking grimly over at the rest of the team. "Everything else is... well, the controlling programs are missing some bits in some places- the crystals containing the code were probably damaged in their last battle or something like that-, but we've still got all the data we acquired from the _Aurora _to fill in what we can right here for a quick patch job, and Atlantis should have enough spare control crystals to sort out the rest- we've got everything we _need _to get this ship going, even if I wouldn't recommend getting into a fight any time soon until we've had time to test the other systems-, but without sublight engines-"

"Is the hyperdrive still working?" Sumner asked, hoping that the apparently-obvious solution that had just occurred to him didn't have some complication that he wasn't aware of that would prevent it from working.

"Well, everything's pretty much there- like I said, there's just a few blank bits of code to fill in; the program must have degraded a bit over the years-, but-" McKay began.

"Problem solved, then; couldn't we use _that _to get off-planet?" the colonel continued (He just hoped that he hadn't missed a report or something about what would happen if you engaged hyperspace in a planet's atmosphere; he tried to stay up-to-date with the SGC's discoveries, but he still found himself focusing on more planetary-based matters when it came to technological advancement, particularly since he'd never been that interested in commanding a ship himself).

"Well, theoretically, yes, but that's not going to do us much good; we might be able to activate it, but we need to be in motion _before _we can go through a window-" McKay began, before he snapped his fingers in inspiration. "Of _course_!"

"What?" Teyla asked.

"We can use the eruption!" McKay clarified.

"Excuse me?" Sumner said, looking incredulously at McKay as he wondered if the possibility of death had finally driven the scientist insane. "You want us to _use _the _eruption_? By which you mean the eruption of this volcano that we're currently standing in? The eruption that you said would be sufficiently powerful enough to completely render this _planet _uninhabitable-"

"Look, the shields are already in fairly good condition; all we need to do right now is make sure that they _stay _that way long enough for us to pull this off," McKay explained, as he turned around and began to rapidly study the information displayed on another console. "Admittedly, even at full power, we won't be able to take that kind of assault for much more than a matter of seconds after the eruption starts, but if I divert all power that _would _be going to the sublight engines into the hyperdrive, that should be long enough for us to open a hyperspace window that will send us into the upper atmosphere."

"OK, that's... _one_ way we could get out of here; are there... any others?" Sumner asked, looking critically at McKay; as much as he respected McKay's intellect, the issues involved in the timing of that plan weren't exactly encouraging...

"Well, one or two, but since they would rely on me figuring out how to develop the equivalent of a tractor beam in the next few hours and having _Daedalus _pretty much _lift _us out, I'm going to have to say this is our best shot," McKay said, dismissively turning back to the console he'd been studying before he realised that his teammates were glaring at his back.

"What?" he said, turning around to look at them in exasperation. "Look, I've got a plan, and I'm _reasonably _sure that it's going to work; just... give me a little time to run the numbers while _Daedalus _takes the first load of refugees, OK?"

"Fine," Sumner said after a few moments of silently staring at McKay made it clear that the Canadian scientist wasn't going to give him any further information, before he reactivated his radio. "Sumner to _Daedalus_, are you still there?"

"_Colonel Sumner_?" Caldwell's voice replied. "_You've been incommunicado for the last few minutes; is something wrong_?"

"Just got a little bit caught up in brainstorming a few ideas about how to deal with the current situation, Colonel," Sumner replied with a slight smile. "Doctor Weir may not have had time to mention it in her initial contact with you, but it turns out that the Taranians have been working on an Ancient-related project of their own for the last few years; the reconstruction of an _Aurora_-class ship called the _Orion_."

"_Really_?" Caldwell said, apparently impressed with the find despite himself. "_Well, with a ship that large, you should be able to get everyone else out in one trip_."

"Quite," Sumner replied. "Unfortunately, the sublight engines may not be up and running in the time available to us, but Doctor McKay has devised a plan to use the upcoming eruption to help us open a hyperspace window that should allow us to enter orbit; he's just running the numbers for it at the moment."

"_Hold on; 'running the numbers'_?" Caldwell repeated (Sumner suddenly wished he'd come up with a better phrase than that; he must have been spending too much time with the team outside of missions if he was starting to sound that unprofessional). "_In other words, Doctor McKay isn't _sure _that the plan will work_?"

"I just need a bit of time to make sure I haven't missed anything; based on what I've got so far, I'm _fairly _sure we can do this, OK?" McKay said, waving an impatient hand at nothing as he continued to study the console screen in front of him. "Just... see if you can get the first wave of evacuees out of here and I'll be ready to give you the news when you get back."

"_Understood_," Caldwell said after a moment's pause, evidently resigned that he'd been told everything he was going to get about the current situation. "_Call back when you've got everyone organised. _Daedalus _out_."

* * *

A few hours later, Sumner had to admit that things were actually going fairly well for them, even if he'd recently had to abandon the Taranian control room when the eruptions reached a point where remaining in that area could have been dangerous. With the first wave of evacuees having been successfully beamed up to the _Daedalus_ and even now on their way to Atlantis- they may have even reached the city already if all had gone well-, McKay had completed his analysis of the _Orion_'s systems and had confirmed that everything that needed to be in working order for the plan to work was in the necessary shape. There'd been some tension among a few villagers from the more outlying settlements who'd preferred the possibility of retreating to a more distant part of the continent in the belief that they could outrun the eruption, but when Teyla and Beckett had been able to promise them an alternative evacuation point in the form of the _Orion_, that argument had ended in favour of getting everyone into the Ancient vessel.

Sumner just wished that their plan didn't depend on them waiting for the actual _eruption _in order to get off-planet, but he had to admit that McKay had a point; they had no way of towing other ships along that they could use to lift _Orion _out of the hanger on its own power, the ship had to be moving if it was going to enter the hyperspace window, and the eruption was the only think capable of providing the necessary momentum that he could think of. He'd briefly thought about launching a couple of drones to try and clear the roof away so that they wouldn't need to depend on the shields as much as the current plan required them to, but that plan had been quickly shot down when he'd reminded himself that the resulting debris would just fall on the ship and either damage the hull or deplete the shields, neither of which were desirable at this point.

He'd never admit it on the record, but he definitely had reason to be grateful to the Phantom right now. If it hadn't been for his previous efforts in helping the Taranians complete what repairs they could on the _Orion_, the ship would probably be nowhere near ready for them to use her in this kind of situation; even in a best-case scenario, he doubted that McKay could have carried out enough repairs even to allow them to survive the eruption, never mind get off-planet afterwards...

Admittedly, he still wished that the Phantom had told them about the _Orion _before now- it might have come in useful during the siege last year, among other things-, but criticising the vigilante in question wouldn't exactly accomplish anything at this point; the masked man had shown time and again that he could easily evade any attempts to capture him while always coming through for them when his aid was genuinely required.

All that Sumner could do was focus on the task at hand and hope that the Phantom wasn't concealing anything else that might have been important earlier for whatever reasons he had for keeping secrets.

God, was it so hard for that man to take orders from a superior officer? He somehow doubted the Phantom had any actual _training_, given the relatively haphazard manner of most of his combat strategies and methods from what he'd seen of the other man in the past; Ronon might have a fighting style that favoured power over finesse, but given the life he'd lived and the foes he'd faced that was almost to be expected, and he still showed some degree of training behind it all...

As much as he acknowledged how the Phantom had helped them in the past, they'd get a lot more done if the Phantom would just make himself accountable and available to them on a regular basis; he might not be 'comfortable' doing that, but they needed to know what he could actually _do _if they were going to successfully defend Atlantis, not just rely on his as some-!

"_McKay to Sumner_," a voice said over the radio.

"Go ahead," Sumner replied, grimly hoping that the Canadian scientist had better news for him.

"_We've managed to get most of the people into the _Orion_, but the tunnels leading to the ship from the settlement have collapsed_," McKay replied, his voice grim as he spoke.

"Was there anyone left in the settlement?" Sumner asked, his fingers crossed at the implications of that particular turn of events; judging by the time since the _Daedalus _had departed, there was still time for the ship to get back here to pick up anyone who might have been trapped on the wrong side of the tunnel...

"_Teyla and Ronon were trying to collect the last group_," McKay replied, eliminating the brief hope Sumner had that it wouldn't be anybody significant missing; Teyla and Ronon might not be official members of the expedition- they didn't even have any 'rank' to speak of, and their position in the city command structure was sketchy at best even if Teyla had done a decent job in charge of Atlantis during their return to Earth after the siege-, but the loss of Teyla's diplomatic skills and Ronon's combat-based knowledge of the Wraith wouldn't exactly be something they could lose easily.

"Based on last count, how many were still out there?" he asked, trying to bring his mind back to the wider issues facing them right now.

"_Apart from Teyla and Ronon, a couple of hundred or so; I had Beckett and Norena do a quick crew count using _Orion_'s internal sensors_," McKay replied.

"In other words, nothing _Daedalus _couldn't handle if they get here in time, right?" Sumner asked; the last thing he wanted was to have to deal with more innocent lives on his conscience.

"_Unfortunately, the key word there is _if_- based on the atmospheric sensors there's __dangerously high levels of sulphur dioxide spewing into the air from dozens of fumaroles; it won't be possible for anything to survive out there for much longer-, but if they can stay inside and stay low in what's left of the tunnel they should be able to__ get through the worst of it before _Daedalus _gets back_," McKay replied. "_I'm trying to send the ship a message, but there's too much between us and the surface; a lava flow just covered the hanger door completely_-"

"Is that going to have an impact on our plan?" Sumner asked, his mind automatically flashing to the worst possible outcome of the current crisis; if they were stuck in the _Orion_, he didn't need to be a scientist to know that their deaths would be _very _unpleasant...

"_So long as I've calculated the power available to the shields, we should be all right_," McKay replied. "_If they last as long as I think they will, we should be blown through the roof far enough for me to activate the hyperspace engines; it's only if I'm _wrong _that things get awkward_..."

"Right; so, as long as you're right, we're fine," Sumner said, hoping that he'd concealed the worst of his scepticism at that statement; McKay might have been right about this kind of thing most of the time, but the last thing they wanted was another Arcturus-like mess when they didn't even have a Stargate they could use to evacuate if things turned ugly on them...

"_Pretty much, yeah_," McKay replied, evidently oblivious to the scepticism (Although that could be the result of him ignoring it as much as it being the result of Sumner successfully concealing it). "_Look, if you could just see who you can find out there, that'd probably be a good thing; it's getting a bit warm out there, and given the declining state of the atmosphere in the area I wouldn't recommend staying in the base longer than you have to..._"

"Understood," Sumner said, ignoring the casual manner in which McKay disregarded the chain of command by giving _him _orders in favour of getting the current task finished.

He'd only agreed to go through with McKay's plan because the scientist had seemed fairly confident that he could get this ship in reasonably-working order in the time available to them; if he'd doomed the Taranians because he'd relied on McKay's hunch...

* * *

After a couple of hours of hurried searching had turned up no sign of any other Taranians in the facility- anyone behind those hot doors was almost certainly beyond any help he could offer at this point-, Sumner was on his way to the _Orion_'s bridge after leading the last of his group into the ship, his fingers privately crossed that McKay had lived up to his usual reputation.

Walking onto the ship's bridge, he allowed himself a slight smile at the sight of Beckett, McKay, and Norena sitting at various chairs around the bridge; it didn't guarantee that the ship was ready, but at least it suggested that McKay didn't feel the need to make any last-minute modifications to improve their chances.

"Colonel Sumner!" Beckett said, turning to look at him with a smile. "How's your group?"

"Everyone I could find in the facility has been brought into the _Orion_," Sumner replied, nodding at Beckett in a brief but reassuring manner before he turned to McKay. "How's your plan coming along?"

"Well, we're pretty much ready to activate the shields; I just want to hold it off until the last _second _in case we have any kind of power issues..." the scientist replied, shrugging slightly at Sumner's pointed stare. "Look, no matter what everyone's done to get this ship back into shape over the years, it's still not been used for several centuries; I think I'm entitled to want to be a bit cautious about how I'm using it..."

"Understood," Sumner said, staring intently at McKay. "Just so long as you're confident your plan will work..."

"Oh, no problem at all, really; all we have to do is ride out the eruption for the four seconds necessary for us to open the hyperspace window," McKay replied with a nod. "It won't let us go very far, of course- even with the repairs the Taranians did over the years the computer's just lost too many control crystals to give it the necessary processing power for longer trips-, but it'll definitely be enough to get us into orbit-"

"I'll take it," Sumner said, walking over to sit down in the bridge's central chair as the two doctors and Norena took up position around the bridge. "How long have we got?"

"No way of _knowing_, but we're pretty much ready anyway," McKay said, studying his console urgently. "Inertial dampeners are engaged, hyperdrive's ready, shields are up... we're good to go."

"Right then," Sumner said, reaching over to activate the ship's P.A. system from the control panel on the side of the chair. "Everyone, this is Colonel Sumner. The ship's programmed and ready to enter hyperspace, but you should all strap yourselves in; things are about to get... rough."

"Don't hold your breath; it could happen any time in the next half-hour," McKay said as he sat back in his seat, just moments before the ship began to shudder around them; Sumner vaguely noted Beckett tightening his grip on the handles of his chair as McKay held tightly onto his console, but for a moment there was no sign of any activity...

Then, as Sumner watched the view in front of the ship's observation window, the _Orion _was launched upwards as magma and lava burst through the floor, sending the ship hurtling towards the roof that Sumner could only hope was collapsing above them-

"_NOW_!" McKay yelled.

As Sumner watched, the brilliant orange of the magma was momentarily replaced by the brilliant blue of hyperspace, before he found himself looking at the black of space, stars spread out before them as the familiar shape of the _Daedalus _drifted into view from out of the corner of the window.

"It worked!" Beckett said, voicing Sumner's own thoughts of relief at the sight before them.

It had been a close call, but they'd done it; they'd saved the Taranians, _and _they'd recovered a potentially highly useful future weapon against the Wraith into the bargain.

"You really _are _a genius," Norena said, smiling over at McKay just as Sumner turned around to look at the rest of the people on the bridge.

"Uh... yeah," McKay said, loosening his grip on the console slightly as he noticed that they had survived the blast. "Well... that's... always good to hear..."

"_This is the _Daedalus," Caldwell's voice said over the radio. "_Are there any survivors aboard_?"

"Affirmative," Sumner replied, allowing himself a relieved smile as he took in what had just taken place. "Actually, we have virtually everyone here."

"_Good to know_," Caldwell replied, nodding in approval. "_What's your engine status_?"

"Hyperdrive's potentially accessible, but sublight's out of action until I can do some more work with it, and the computer's lost too much data with the damage it sustained to the control crystals for it to provide the necessary processing power to calculate trips on the magnitude we're facing," McKay put in. "If you could provide us with the necessary equations from _Daedalus_, I should be able to get us back to Atlantis, but it'll take a bit of time to get everything working once we get there..."

"_Just so long as you can do it soon, Doctor McKay, we'll take what we can get right now_," Caldwell said, a slight edge to his voice that set off more than a few warning bells in Sumner's mind.

He might not be saying anything more at this time- not that Sumner could blame him; even if he had just helped to save the Taranians, he didn't want to say anything with Norena in the room that might give them a negative impression of Atlantis's capabilities-, but Sumner was prepared to bet that there was going to be _something _problematic waiting for them...

* * *

AN 2: Well, that's _Orion _recovered; next up, we jump to shortly before the opening scenes of _Allies_, as Elizabeth tries to talk to John about possible strategies to deal with the approaching Hive-Ship...


	22. An Olive Branch from the Wraith

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Mystery of the Phantom

As she stood on the balcony, for what felt like the first time since she'd started this tradition after arriving on Atlantis, the night sky above Elizabeth failed to provide the peace that she'd always sought here originally; the knowledge that there was a Wraith Hive-ship approaching their current solar system tainted the current view for her, no matter how much she recognised that it was still a day or two away from their current location.

Admittedly, their chances in the current fight were a lot better than they'd been when the Wraith had attacked them last year- they had one nearly full Zero Point Module and the remaining dregs of power in the original ZPM, a restocked compliment of drones thanks to their encounter with the Tower after they'd dethroned the Lord Protector, and work on the _Orion _had progressed to the point that the ship was virtually back to full working order-, but that didn't change the facts; if the Wraith _knew _that they were here, they were in serious trouble even if they could defeat this Hive.

There had to be _something _she could do...

"Penny for your thoughts?" a familiar voice said.

"_Now _you show up?" Elizabeth asked, turning to look at John in exasperation; his 'sudden appearance' act might be impressive, but it could also become _very _frustrating when she was already feeling stressed about the current situation.

"It's been a bit hectic over the last few days; I didn't want to risk it-" John began, only for the cool manner in which he began to explain his actions to finally push Elizabeth over the edge.

"Risk what; getting _captured_?" she yelled, walking over to stand almost directly in front of John. She hated to be this blunt almost as soon as she spoke, but faced with the chance to talk with someone who she didn't have to be Atlantis's in-control leader for, the ability to vent was something she couldn't pass up no matter how much she might want to. "We could use your _help _here-!"

"Sumner will only accept that help so long as I do things _his _way; I can't _do _that-!" John began, his voice becoming increasingly frustrated as he looked back at her.

"Why?" Elizabeth retaliated in equal frustration; given that she couldn't just yell at the Wraith or her staff, as much as she hated to sound so petty, John was the best thing available right now. "Because your precious ego won't allow you to accept orders from anyone else-?"

"Because that man is trying to do things by a book that doesn't apply out here; how am I _meant _to react-?"

"You could at least try and _moderate_ your approach-!"

"I DON'T TRUST HIM!" John yelled.

For a moment, silence settled over the balcony as the two leaders- both official and unofficial- stared at each other, until John sighed.

"I'm sorry," he said, looking apologetically at Elizabeth. "I didn't... look, whatever that might have sounded like, I _do _trust _you_; I just..."

"No, _I'm _sorry," Elizabeth said, trying to smile reassuringly at John. "I understand why you have issues with Sumner's authority, but it's just... it's been so _busy _here these last few days; getting the _Orion_'s repairs finished, evacuating the Athosians back to the mainland, setting up the cloak again..."

She shook her head in exasperation. "I guess I... I needed to vent at something, and you were the closest thing available; everyone else needs me to be in control, needs me to take command of the situation, needs me to be something that I'm not-"

"No," John interrupted, walking over to turn Elizabeth away from the balcony and face him, placing his hands on her shoulders as he looked at her. "They need you to be who you have the _potential _to be. There might be some debate back at Stargate Command, but you wouldn't have been given this job if the right people didn't think you could do it; you just need to _believe _in yourself-"

"When nobody _else _does?" Elizabeth asked, sighing in frustration as she lowered her head. "Half the time I'm with him I feel like Sumner only takes orders from me because he has to according to the chain of command established by his superiors, I can barely spend any time with the rest of my staff because Sumner wants us to remain professionally detached from the people we may have to order to their deaths at some point, Rodney spends most of his time in his lab when he's not on missions- I'm not sure if he even _has _any spare time any more; he's either working, eating or sleeping-, Teyla and Carson are friendly but they have to focus on what her people and his department need rather than spare the time to spend time with me, and Ronon... well, I don't think I need to tell _you _why that's difficult..."

Shrugging his hands off her shoulders, she turned to lean on the balcony once more, staring out at the ocean before her as though looking for the answers, before she spoke again. "I just... I wish I felt like I was here because people genuinely believed that I could do the job, not because I was just the most politically viable choice..."

"I believe in you," John said simply.

"_Why_?" Elizabeth asked, turning to look at him once again; for a moment, their proximity made her flash back to their brief encounter while Phoebus had controlled her body- she'd never mentioned that moment and she never would unless John showed a willingness to discuss it first; Phoebus's implications had been... 'confusing' was the most obvious word-, but she pushed that thought aside to focus on the relevant question. "Why do you have such... _faith _in me?"

"Because since you came here, you've never chosen the course of action that works best for Earth, but always gone for the course of action that works best for _humanity_," John said solemnly (Something in his stance suggested that he was keeping something back, but after the trouble she'd had getting John to talk about himself in the past she wasn't going to push him to provide more information than he wanted to). "We have soldiers, scientists, and doctors here, each one playing a role that they feel is more important than the others, but you're able to stand apart from all that and find a way to make them all work together to help those who need it, both here _and _back on Earth."

For a moment, as he looked at her, Elizabeth thought that he was going to say something- she wasn't sure what, but he was definitely about to say _something_-, but then he shook his head slightly and continued with something that sounded slightly forced to her, as though he'd changed his mind on what he was about to say at the last minute. "Even if some people on Earth don't get that because they're too removed from this situation... _I _have faith in you, and more than a few of the staff here feel the same."

For a moment, Elizabeth wasn't sure what to say in response to that statement- the sheer simplicity of John's sentence was somehow all the more overpowering than his earlier shout had been; he spoke as if her ability to command Atlantis was a simple fact of the universe-, but, in the end, her mind's role in the decision-making process was seemingly bypassed as she wrapped her arms around John and gave him a brief hug.

"Thank you," she said, kissing him briefly on the cheek that was the only part of his face exposed by his mask- she wasn't sure why she did that, but it just felt... _right _to do so- before she stepped back to smile at him. "I... I needed that."

"You're welcome," John replied, a slight softness in his eyes as he looked at her that she hadn't seen before and couldn't quite interpret.

For a moment, as Elizabeth looked back at him, she almost didn't see the mask or whatever he had underneath it- the memory of the smooth surface she'd felt when Phoebus had extended her fingers under the mask still unnerved her, but she was willing to leave that particular secret for whenever John felt the time was right to share it with her-; she just saw the man who had done so much for Atlantis, the man who had fought for this galaxy before they knew there was anything to fight here... and the man who believed in her when she had trouble believing in herself...

"Anyway," John said, smiling slightly at her as he stepped back towards the balcony, "I'd better get into position before that hive gets here."

"Position?" Elizabeth repeated.

"Hey, I've got more practise with that control chair than anyone here; if we get into a fight, I think you'd want me in charge of that thing rather than anyone else," John said, shrugging slightly with the nonchalance that you could only show when stating a fact before he smiled at her. "And don't worry, I won't do _anything _to try and take charge unless we get into a battle and I'm sure I'm needed; I don't want to provoke anything if I don't have to..."

Elizabeth only gave John a nod of approval after he proposed his idea, but was all that he needed. As soon as her head had inclined in acknowledgement, he had turned around and jumped off the edge of the balcony, his cape spreading as he fell towards the lower levels, leaving her to turn around and walk back into the city, fighting the urge to smile.

The news that the Phantom was still watching out for them might not be something that Sumner would regard as especially encouraging, but for Elizabeth, John's promise that he would be there if they needed him was all they needed right now...

* * *

A couple of days later, as she stood in Atlantis's control room, preparing to coordinate the city's current defence plan against the Wraith, Elizabeth could only hope that John's intervention wouldn't be required; _she _might recognise that he'd only do that kind of thing if he felt that he absolutely had to, but that didn't mean that Sumner would be as understanding about it as she would be...

She knew that she was just trying to focus on the smaller-scale issues to avoid thinking about the long-term issues facing them- even with their new control of the _Orion_ after the Taranians had allowed them control of the ship, they still hadn't had the time to fully test the new control crystals or any of the code that was on them-, but she couldn't help it; there was so little that she could actually _do _right now...

"All of my people have been safely relocated to the city," Teyla said as she and Ronon hurried into the control room

"Did everything go smoothly?" Elizabeth asked; she hated having to relocate the Athosians like this, even if Halling and Teyla continued to assure her that they were grateful for the chance to help Atlantis.

"Yeah; they're pretty used to it, back and forth, by now," Ronon said dismissively. "Have you picked up any of their contacts?"

"Sergeant?" Elizabeth asked, glancing at Chuck as he sat at the console (It was somehow harder to think of him by his rank).

"Negative, ma'am," the young man replied after a quick glance at his laptop. "Scans are still clear. It looks like it's just the one hive ship."

"And our cloak?" she asked.

"Up and running," Chuck confirmed. "All readings are in the clear."

"Good," she said, before she reached up to activate her headset radio. "Colonel Caldwell, are you in position?"

"_Affirmative_," Caldwell's voice replied. "_We're out of scanning range and ready to jump into position on your go-ahead_."

"Excellent," Elizabeth replied.

"_Just for the record_," Caldwell added, "_I still think that we should be in orbit around Atlantis, ready to open up on that hive ship the second it comes out of hyperspace_."

"It's one hive, Caldwell, which suggests they might just be checking up on us," Elizabeth replied (She wouldn't even admit it to John, but it still left her feeling slightly frustrated her when Caldwell did that kind of thing; did he honestly think she hadn't considered this whole situation from a military standpoint rather than just trying to determine the best way to avoid a fight?). "There's no need to confirm our presence if we don't have to. Just stand by."

"_Standing by_," Caldwell replied, terminating the connection at his end as Elizabeth turned her attention to another matter.

"Colonel Sumner, what's your status?" she asked, shifting her radio from the _Daedalus_ to the frequency that she could use to contact the _Orion_.

"_We're out of sensor range and ready to jump into hyperspace on your word_," Sumner responded, his tone grim. "_McKay still has some doubts about _Orion_'s ability to accurately calculate short-range jumps- something about him having more time to compensate over longer distances-, but the ship seems to be ready for combat, so we shouldn't have to worry about _that _if nothing else_."

"Well, hopefully we won't need you; just... be ready in case we do," Elizabeth said, before she terminated the connection and turned to look at the technician.

"I have a contact," Chuck said, looking grimly back at her as he studied his laptop for a moment. "It's going into geosynchronous orbit; hasn't armed any of its weapons."

"If they do, I want you to switch from cloak to shield as quickly as possible," Elizabeth said. "Don't wait for my order."

"Yes, ma'am," Chuck replied (Elizabeth was grateful for his casual acceptance of that order; whatever importance Sumner might place on the chain of command, it was always good to see them showing independent thought).

After a few moments of silence, during which Elizbaeth could only stare at the screen displaying the current status of Lantea, Chuck glanced around at her. "Transmitting a signal, audio only."

"Put it on speaker," Elizabeth said, her gaze still fixed on the red dot representing the hive-ship.

"_We know you are there_," a male voice said over the radio. "_We mean you no harm. Please respond_."

"Colonel Sumner," Elizabeth said, her voice low as she activated the radio to address _Orion_, "are you hearing this?"

"It's repeating again," Chuck said before Sumner could respond (Although he could equally have been just as stunned into silence as she had almost been).

"_We mean you no harm_," the voice said again. "_There is no point in hiding, Doctor Weir_."

Elizabeth couldn't help but start at that particular statement; the idea that someone in a Wraith ship could address her by name was _not _encouraging for her hope that it was someone else they were dealing with...

"_We know you are there_," the voice continued to say. "_We mean you no harm. Please respond_."

"_Is that who I think it is_?" Sumner asked at last.

"He's addressing me by name," Elizabeth replied grimly. "I think we can assume it's Michael."

She might have expected their flawed experiment with the retrovirus to come back to haunt them eventually, but she'd assumed that it would have taken more time than this; even if he hadn't been killed by the Wraith, would they really listen to someone who couldn't even remember his past?

"_You don't actually intend to respond_?" Caldwell said, clearly having been listening to the transmission himself.

"Why not?" Elizabeth asked.

"_Where do you want me to start_?" the _Daedalus _commander replied

"I think we can safely say our cover is blown," Elizabeth pointed out, deciding to tackle the most obvious problem facing them right now.

"_I wouldn't jump to that conclusion_," Caldwell said with a slightly dismissive tone.

"The message is from Michael, Colonel," Elizabeth retorted; it was hard to deny that kind of evidence, no matter how much they might want to do so.

"They know we're here," Ronon said with his usual direct manner.

"_But they don't know exactly where we are_," Caldwell pointed out.

"_He's right_," Sumner added, having evidently been listening to the conversation from _Orion_. "_If we answer them, we provide them with a means of directly targeting Atlantis; we can't risk it_."

"Teyla?" Elizabeth asked, looking hopefully over at the Athosian; relying on telepathic contact might make her uncomfortable, but if it could get the job done in this current situation...

"Any attempt on my part to connect with Michael will confirm our location as surely as if you answer by radio," Teyla replied, dashing Elizabeth's brief hope that she might have found a loophole in the current dilemma.

"_I recommend you open a secure channel to the hive via the _Daedalus," McKay put in from _Orion_. "_That way they won't be able to pinpoint Atlantis' position_."

"And we can always turn the shield on," Elizabeth finished for them.

"_We have more than enough firepower to stop one Hive if things get ugly; I say we keep it in reserve and try McKay's suggestion_," Sumner pointed out.

With options limited, Elizabeth turned to look at Teyla and Ronon; it was probably a long shot, but if anyone was going to know the answer to the question she had right now, it was probably them.

"Have you ever heard of a Wraith behaving this way?" she asked; her hopes for a positive answer weren't high, but this wasn't the time to worry about that.

"No," Ronon replied.

"Nor have I," Teyla added.

"Right," Elizabeth said, putting aside her disappointment at the lack of past experiences to draw on to focus on the immediate issue. "Let's hear what they have to say."

* * *

As John crouched in his 'hiding-hole' just outside the control chair, his earpiece tuned into Elizabeth's so that he could hear whatever was about to be said- it didn't count as eavesdropping if he was only going to do this kind of thing to stay informed in an emergency; he'd never do something like this to listen to her in private-, he couldn't help but wish that he'd considered the possibility of this particular Wraith coming back to haunt him so quickly.

God... _Michael _was still alive...

He'd been hoping that the Wraith would have killed the guy as a freak the moment they had him back in their custody again- even if the retrovirus hadn't been able to permanently transform him into a human, the experiments he'd undergone before being exposed to the drug itself had to have done _something _to his system that would make it hard for him to become a normal Wraith again-, and here they were, facing the one guy he'd _really _hoped they'd seen the last of...

The fact that they weren't bringing him down to Atlantis at least made him feel slightly better- the less opportunities for Wraith to gain access to Ancient technology the better-, but he still didn't exactly feel that relaxed about this current mess; Zelenka's preparations for setting up an indirect communication link sounded like they'd be effective, but that didn't make him feel that much better as Elizabeth gave the order to open the channel.

"_Hello, Michael_," Elizabeth's voice said, confirming all of John's worst thoughts about the current mess.

"_Why the long delay_?" Michael's voice responded.

"_We needed to take a few precautions before contacting you_," Elizabeth clarified. "_I'm sure you understand why_."

"_I said we would not harm you_," Michael said (John wasn't sure if he should feel stunned or awkward about the fact that Michael had that much faith that they would keep their word after what he'd said the last time they were on the same planet).

"_Well, excuse me for not taking you at your word_," Elizabeth responded (John couldn't help but hate himself at that comment; just two years in the Pegasus Galaxy had turned the most peaceful woman he'd ever known into someone who doubted other people's words, no matter how justified that doubt was). "_You wanted to talk; we're listening. Go ahead_."

"_Over two years ago, every hive ship in this galaxy emerged from hibernation prematurely_," Michael replied, his voice slow and grim, as though he was having trouble even remembering this; clearly the retrovirus's mental effects hadn't gone away yet. "_We thought a new rich feeding ground had been discovered_."

"_Earth_," Elizabeth said, John's own lips moving almost automatically to repeat her statement as he processed the implications of that statement (It was one reason he'd always taken care not to give any Wraith the chance to interrogate him; after everything the other Elizabeth had told him about the Wraith's psychic powers, he hadn't wanted to risk them reading his mind and learning about his _real _homeworld).

"_Unfortunately_," Michael continued, "_locating your planet and uncovering an effective means of transportation to get there has proven quite difficult_."

"_Well, I can't say I'm sad to hear that_," Elizabeth responded, a slight smile in her tone.

"_For the first time since the dawn of our race, there are too few of your kind to feed the waking Wraith_," Michael continued. "_This has resulted in civil war. Hives are forming alliances. The strong are attacking the weak_."

"_Which are you_?" Elizabeth asked (Whether just trying to establish their social position or get a better idea regarding how many more Hives they might expect to show up if they dealt with this one, John couldn't be sure).

"_Our goals are not dissimilar, Doctor Weir_," Michael replied, ignoring the offered question.

"_You would like to eliminate the Wraith as a threat_?" Elizabeth asked, her incredulity obvious. "_I find that hard to believe_."

"_We would like you to give us Doctor Beckett's retrovirus_," Michael clarified. "_If we were able to distribute it among the rival Wraith hives in sufficient quantity, this would both render them helpless and provide us with an alternative food source_."

John wasn't sure if he should feel enthusiastic or sickened at the scenario that Michael had just proposed; Elizabeth's comment about the Wraith becoming humans certainly presented an interesting new solution to the current conflict by having the Wraith destroy themselves, but even if Michael seemed to like that idea, John couldn't shake the thought that there was going to be some kind of catch...

"_As a sign of good faith, I am sending you our jamming codes_," Michael continued, the offer drawing John's attention back to the conversation. "_This programme was established and distributed before the civil war broke out, so we assume all the hive ships are still using it. By figuring out how to bypass or disable this programme, you would be able to beam your nuclear weapons aboard any of our ships whenever you so please_. _We are willing to help you achieve this if you help us_."

John vaguely heard a console beep and a technician apparently confirm that they were receiving the aforementioned data burst, but the range of Elizabeth's radio wasn't sufficient for him to actually explicitly hear what was being said, even if her subsequent comment about sending something to a non-networked computer suggested that they'd sent the data they'd just mentioned.

"_I'm sure you'll want to recall all the ships you have lying in wait for us and discuss this with your people_," Michael continued, his tone rather casual for such a potentially dangerous topic. "_We will await your reply... but, should you make an attempt to destroy us, we will alert every Wraith in this galaxy to the fact that Atlantis is still very much intact. I'm sure you wouldn't want that_."

With that, Michael terminated the connection, leaving John with nothing to do but sit grimly in his hiding-place before he began to move.

If what he'd heard was any indication of what he could anticipate in the future, he should probably be near the conference room to hear how things were about to go...


	23. Forging Questionable Alliances

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: I skipped over the conference to discuss Michael's proposal because it wasn't that different from the original version- the only real difference is that Sumner didn't ask Teyla for her thoughts on the plan because, unlike Sheppard, he doesn't particularly care about that issue-, and I felt that subsequent developments after the Wraith arrived on Atlantis would be more interesting to explore anyway (As always, anything you don't see happened pretty much like it did in the show, and I'll try and provide some detail on what happened there where appropriate)

Mystery of the Phantom

As Elizabeth stood in the control, apprehensively waiting for the Wraith 'delegation'- she almost wished that she could go back to the days when she believed that kind of thing was possible; a part of her felt like a sheep waiting for the wolves to show up in her pen. Even with Orion available as a secret weapon and Sumner and Ronon's rare joint approval of their current plan- Ronon's independent nature could cause a few clashes between the two men at times-, she couldn't shake the feeling that _something _was going to go wrong at some point.

God... she couldn't even call John here for security because of the risk that he'd provoke the Wraith into an attack given their past 'relationship' with him; John had made it clear that he barely accepted Michael's presence when he'd been human, and she didn't even _want _to imagine what he could do if he thought things weren't going their way...

The strange thing was, when she thought about it, what Elizabeth wanted the most right now wasn't for John to be present because of the additional security that it would provide her with; she just wanted John present for _him_.

She was engaged in diplomatic negotiations that could end or at least seriously curtail the Wraith's expansion in this galaxy, and she wanted a masked vigilante with little apparent restrictions against killing to be there for _moral_ support...

Then the Wraith delegation walked into the control room, including a short-haired Wraith with slightly greenish skin that could only be Michael, a more conventional Wraith, and a Wraith female with long dark hair dressed in white, and Elizabeth's wishes had to be put aside to focus on the task at hand.

She and Sumner had already prepared a list of 'rules' for the Wraith to follow that hopefully wouldn't be too restrictive for them; she might want to make this potential alliance work, but she didn't need to have John there to remind her that trusting any Wraith for longer than was absolutely necessary probably wouldn't be the smartest thing she'd ever done.

"I'm Doctor Elizabeth Weir," she said at last, hoping that she looked more confident than she felt; for all the preparations that they had made and were about to make, this kind of situation was definitely one for the record books, and the problem with setting precedents like that was that it was hard to know what would trigger a mistake. "Welcome to Atlantis."

* * *

As he kept a relatively constant eye on various members of the Wraith 'delegation'- Michael remained his top priority, although some of the Wraith scientists attracted his interest as well-while crawling through the tunnels, John wondered if he should feel guilty at the lack of trust he was showing them when so far they'd done nothing while he was watching them to show that he had any reason to be suspicious of them.

They'd agreed to Elizabeth's terms and restrictions relatively easily in exchange for the chance to work on the retrovirus, Zelenka and Beckett's discussions with the Wraith scientist about dissemination appeared to be going well- even if they were still having trouble working out _how _they were going to effectively disseminate the retrovirus in a gaseous form throughout a hive-ship-, and McKay's analysis of the Wraith data that they had received earlier seemed to be going well based on the reports he'd heard (Even if Hermiod- he wished he'd had a bit of time to talk with that Asgard guy about stuff, but sometimes you had to ignore what you wanted and focus on what was practical- apparently wasn't that enthusiastic about it, given his race's own level of technological advancement compared to the Wraith).

Right now, however, the Wraith that was currently occupying his attention was Michael, who was currently simply waiting around in the same isolation room where he had been kept after he had originally been brought to Atlantis all those weeks ago, examining the bed where he had been kept with an almost affectionate manner as two marine guards stood on either side of the room.

Looking at him now, John had to wonder how much of the retrovirus-induced memory-loss remained; Beckett had calculated that repeated reinforcement of his 'new' identity would have eventually resulted in Michael forming new memories to supplant his old ones and support what he was being told about his past, but the scientist had never gone into much detail about what he'd recall if he started to return to his original biology...

"Hello, Michael," a voice said; glancing over at the door from his silent 'observation post' behind the maintenance hatch, John wondered if he should feel relieved or worried that it was Teyla and Ronon standing there.

On the one hand, they could definitely handle Michael better than most if things turned ugly, but on the other hand, they'd acquired the ability to handle him so well by living in a galaxy where they constantly had to fight the Wraith; instinct was a tricky thing to overcome in this kind of situation (Not that he thought he'd be better-equipped at suppressing his hatred than they were; he just felt that he'd be able to focus more on his dedication to Elizabeth and her goal than that, while they didn't _really _have anything to focus on to the same extent).

"It seemed right to come back here, and to see you," Michael said, his tone almost wistful as he looked over at Teyla. "Thank you for coming."

As he paused to lean forward slightly on the bed, Michael nodded at where Ronon stood slightly off to the side behind Teyla, the Satedean's posture seemingly relaxed but still obviously ready for a fight. "You didn't have to bring him."

"I insisted," Ronon said simply.

"The last time I saw you," Michael said, addressing Teyla without responding to Ronon, his tone matter-of-fact at first with a slight hesitancy about it as he continued, "I really was going to feed on you, but it was not a matter of choice. It was... instinct."

Judging by Teyla's neutral expression, she didn't accept that as an explanation any more than he did; instinct could be overridden, particularly since Michael hadn't really possessed much in the way of conscious memory of what he'd once done to survive at the time.

"That is what you have come here to say?" she asked, a pointed tone in her voice as she spoke.

"You have given me... a very rare perspective among the Wraith," Michael said, sighing contemplatively, still sounding almost disturbingly wistful about the current topic. "Few of us have ever come to know the humans we are going to feed on as anything more than a means to survive... and still, I would do what I had to do. But what you did to me-"

"We did the same- to survive," Teyla interjected.

"I thought you were trying to help me," Michael countered, an obviously hostile tone to his voice.

"What's your point?" Ronon asked bitterly.

"We're not as different as you think," Michael said.

"We are nothing like you," Teyla said simply, glaring at the former 'lieutenant' even as he laughed briefly at her response (Not that John could blame her for her anger; what had been done to Michael might not have been totally acceptable, but it wasn't like they'd grabbed someone who couldn't defend themselves and who'd done _nothing _to them beforehand just for their own benefit).

"You are a lot more like us than you allow yourselves to believe," Michael responded, after he had stopped laughing at Teyla's last comment.

"I will not argue with you, Michael," Teyla said resolutely. "It is pointless."

"If we are to make this alliance work, we must both overcome the instincts that define us," Michael said, only to be met with nothing but stares from Ronon and Teyla at his comment. "We will not meet again."

"Goodbye," Teyla said, Michael simply inclining his head at her as he repeated her farewell. For a moment, as Teyla turned to leave the room, John thought that things were going to work out, but then Ronon pulled out his gun and held it to Michael's head, snarling in obvious rage, as soon as Teyla had left the room, and even Michael's nonchalance wasn't enough to make him feel better about it.

"You're proving my point right now," Michael said, his face apparently neutral as he looked back at Ronon. "Oh, every fibre in your body wants to kill me-"

"But he's _not_," John said, stepping out of his tunnel- it was fortunately at the end of the bed hidden behind a few pieces of equipment, so the marines at either end couldn't see _exactly _where it was even if they quickly raised their weapons slightly as he appeared- and glaring at the Wraith that had once been a man. "And _that's _what makes the difference between him and you."

"Phantom..." Michael said, his eyes flicking over to look at him with a slight smile even as he continued to face Ronon. "Are _you _here to kill me?"

"No," John replied, shaking his head as he folded his arms and stared at the other man. "I'm here to point out to you why you're wrong; Ronon is a victim of his instincts, but unlike you, he doesn't let them define who he is."

He smiled slightly as he glanced over at the Satedean, even if Ronon's gun was still pointing at Michael, before he turned his attention back to the former Wraith. "And that's why what we are is something _you _couldn't be; even when you didn't _know_ what you were, you tried to go back to that, but Ronon is at least trying to be more than just some guy who kills Wraith."

Ronon didn't respond verbally to John's comment, but the brief nod he gave him before he turned and walked out was enough for him.

"You have a lot of faith in these people," Michael said, looking at John in a slightly quizzical manner.

"They wanted to find a way to end this without having to kill people," John replied with a slight shrug, ignoring the marines around him (He noted that they were at least still more obviously apprehensive around Michael rather than him; at least his past record counted for _something_). "Just because I've destroyed hive-ships in the past doesn't mean I want to make a habit of it; if they can stop the Wraith without us having to kill them, I'm all for that."

"Even if it means working with me?" Michael asked, raising an eyebrow slightly as he looked at John. "You have already made your feelings towards me clear..."

"I never said that I automatically hate all Wraith, Michael; I just meant that I'm a lot less inclined to sympathise with a Wraith than I would be with a human," John clarified, continuing to glare at the hybrid as he spoke. "You're not trying to kill anyone, and your plan seems genuine enough; just know that, if I get so much as a _hint _that you're up to something, I will be down on you like the metaphorical ton of bricks, understood?"

"Bricks?" Michael repeated with a slightly uncertain smile, as though he had stumbled across something interesting when he wasn't sure what it meant.

"The _point_," John said, his eyes narrowing as he glared at Michael, "is that I _will _take you out if I think that you're going to betray us; is that clear?"

"Perfectly," Michael said, nodding at John with a slight smile that John didn't like the look of.

He knew that he was probably being overly paranoid, but he couldn't help it; when dealing with a Wraith like Michael- even if he wasn't a _full _Wraith any more- who clearly demonstrated an ability to think about a bit more than where his next meal was coming from, he felt that he was allowed to show some concern about what the guy could realise if he was given too much information...

* * *

"What will happen once you disseminate the weapon?" Elizabeth asked, looking at the Wraith Queen as she sat on the other side of Elizabeth's desk, Sumner currently standing just behind the Queen along with the two marine guards.

It might have been a somewhat dangerous position to be in- guards or no guards, Wraith were _fast_-, but Elizabeth had wanted to have a chance to question the Queen without any other Wraith around, and the long-term consequences of their current plan were something that Elizabeth didn't feel comfortable ignoring.

"We shall continue on to the next hive," the Wraith Queen replied casually.

"And then what?" Sumner asked, as he walked around from behind the Queen to stand alongside her.

"We will continue until we have conquered all of our enemies," she said in the same casual tone.

"And you think our retrovirus can do all that?" Elizabeth asked, leaning forward to look pointedly at the Queen.

"Yes," the other woman- Elizabeth couldn't think of her as something 'other' in an environment like this, even as she acknowledged that the figure before her wasn't human- said, with a slightly wicked smile that reminded Elizabeth uncomfortably of the stereotypical image of a vampire.

"And once we've handed it over to you, how can we know that you'll leave it at that?" Sumner asked.

"I see," the Queen said, her expression neutral as she looked at Sumner before returning her stare to Elizabeth. "Your people will... not be harmed. Such will be the nature of our agreement."

"And what about all the other humans on the other worlds?" Elizabeth asked. "Any chance you'll stop feeding on them?"

"Your retrovirus will allow us to feed off enemy Wraith," the Queen pointed out. "There will come a time, however, when our enemy will be vanquished."

"At which point you will resume feeding on the human population of this galaxy," Sumner said, his tone grim as he looked at the Queen.

"That will take far longer than your short lifetime," the Queen interjected.

"Let's just assume that I'd prefer to ensure my successors don't have to clean up my mess after I retire," Sumner replied.

"The technology of this city- this city that you now control- is far more powerful than that of the Wraith," the Queen said, initially looking at Elizabeth before she turned her gaze to Sumner, "yet we brought the Lanteans to their knees. Why?"

"Weight of numbers, based on what we've found in the database," Sumner said.

"Numbers that will be diminished by your retrovirus," the Queen said with a slight shrug. "Balance will be restored. I believe that is as much as either of us can ask for, don't you?"

Elizabeth hated the thought that the best they could do was restore a sense of balance, but in one sense the Queen had a point; right now, keeping the Wraith focused on each other so that the human population of Pegasus had a chance to grow stronger was the best that she could hope for.

If only their original plan for the virus was still possible; eliminating the Wraith need to feed was something she would have been a _lot _more comfortable with...

* * *

As he and the rest of the city waited for news about how their latest research project had turned out, John had to admit that things seemed to be going fairly well. With Beckett and the Wraith scientist having effectively devised a means of dispersing the virus as a gas rather than the injections they'd used earlier, the subsequent test had apparently been a fairly effective success- even if John _really _didn't like how the Queen had just killed her now-human crewman so abruptly; even the Wraith should show some concern about their fellows in his book-, and he was currently waiting, along with the rest of Atlantis, for news on the planned attack on another hive-ship in their immediate vicinity.

He might not be comfortable with the plan, but if they could even get one more hive-ship off the table in this whole conflict, that would be something; it wasn't like those things could reach their peak _that _easily, after all...

"Carson," Elizabeth's voice said, drawing John's train of thought back to his current location; with a few Wraith still in Atlantis, and knowing that this was the best location to wait in to be up-to-date with the city's current activities, he had chosen to wait in the tunnels near Elizabeth's office to keep updated on what was happening.

"Elizabeth," Beckett said, John looking out from his tunnel in the wall behind Elizabeth's just in time to see the Scottish doctor put his hands on the desk and lean over, prompting Elizabeth to cease her earlier typing and look back at him. "When I developed this retrovirus for the Wraith, it was to free them from what I perceived to be an unnatural state. Now, at the very moment they take human form, they'll face a horribly painful death. No matter how we rationalise this, we're still lettin' the Wraith kill humans."

"Well, I guess it depends on how you define 'human'," Elizabeth replied, even if the uncomfortable tone in her voice made it clear to John that she wasn't happy about that questionable assessment any more than Beckett was.

"We can't judge an entire race based on the fact that Michael's experiment didn't work," the doctor replied; John wondered if he should approve or simply be frustrated at the other man's dedication to the Hippocratic oath.

"If you're asking me whether or not I'm losing sleep over this..." Elizabeth began, before the expression on Beckett's face made her pause and look down before continuing. "Well, I am taking those sedatives you prescribed."

Somehow, the simplicity of that statement broke John's heart where Beckett's saddened expression had done nothing.

The woman he'd vowed to protect was in a position where she felt it necessary to _drug _herself in order to get a good night's sleep...

Damnit, _he _was supposed to be the one to make the hard choices like this so that she wouldn't have to; was it asking too much for the universe to spare her from that kind of crap?

She was meant to be leading this expedition in a journey of discovery and exploration of the secrets of a whole new galaxy; she was _not _meant to be doing... _this_!

John didn't bother sticking around; turning around, he began to crawl back towards the nearest tunnel intersection so that he could find somewhere large enough to get slightly more comfortable, and then settle down to mourn his failure.

No matter how much he tried to do so, he couldn't escape the fact that Elizabeth had been forced to do things she should never have had to do since she became the commander of Atlantis...

* * *

When the news came in that the planned attempt to disperse the retrovirus gas throughout the hive had failed, Elizabeth wasn't sure if she should even bother being surprised; it seemed to practically be a rule that any attempts to activate a superweapon would be difficult at first, no matter how much you wanted things to go smoothly (Even if that rule at least meant that _they _couldn't be wiped out by their enemies on the first attempt as well).

"_Our delegation was searched_," the Wraith Queen explained over the video feed, Sumner and McKay standing with Elizabeth as they stared grimly at the screen. "_They were killed immediately when your canisters were discovered. Our transport ship tried to escape but it was destroyed. You_ must_ devise a better delivery method_."

"Or what?" Elizabeth asked; she was fairly certain she knew, but she preferred confirmation.

"_Or we will disclose your location to the other Wraith_," the Queen said, her face presenting that same frustrating smirk that reminded Elizabeth of the teenage beauty queens who'd always mocked her dedication to her studies.

"We kept our part of the bargain," Elizabeth said (She was actually slightly grateful she'd spent so much time with John by now; he could deliver a hard stare that it was very useful to imitate at times like this). "We gave you the retrovirus."

"_And it is useless without an effective delivery system_," the Queen retorted angrily.

"Alliances are normally more 'give and take' than this; do you seriously expect us to do _all _the work to get this virus working properly?" Sumner put in from alongside her, only for the Queen's subsequent glare at them to leave Elizabeth forced to turn her attention over to McKay out of a lack of any idea what she could say to the Queen's admittedly logical point.

"OK, OK," McKay said, sagging and sighing in resignation. "I will figure something out..."

As soon as he'd spoken, McKay seemed to collect himself as he re-focused his attention on the Queen, an arm outstretched as he pointed at the screen. "But no more holding back. I want to know everything there is to know about hive ships; schematics, power distribution, life support configurations, everything you've got."

"_Then you shall have it_," the Queen said, in such a simple tone of voice that even Elizabeth was surprised to hear.

"For real?" McKay said, evidently just as stunned as she was at the casual acceptance of that demand.

Without answering verbally, the Queen turned her head and apparently nodded at someone off-camera, followed swiftly by a console beeping behind Elizabeth.

"Receiving transmission," Chuck said.

"Make sure it's secure," Elizabeth said as she glanced over at McKay.

"Yeah-yeah-yeah, we're completely firewalled; let me see that," McKay said, running over to Chuck's station and shoving him out of the way, ignoring the chair rolling away from the console as he stared at the screen in amazement for a few moments before he looked eagerly back at Elizabeth and Sumner. "She actually did it! I mean, this is the motherload!"

"What is, exactly?" Elizabeth asked, looking at McKay even as Sumner kept his gaze on the screen.

"Only everything you've ever wanted to know about Wraith technology but were afraid to ask," McKay replied, grinning broadly as he turned back to study the screen, leaving Elizabeth and Sumner to return their attention to the Wraith Queen

"Why are you doing this?" Elizabeth asked, her eyes narrowing slightly as she analysed her 'counterpart' in the current alliance.

"_We have suffered extensive damage_," the Queen replied.

For a moment, Elizabeth exchanged glances with Sumner, but even the warning in his eyes wasn't enough to discourage her from her next decision; if they were going to maintain their alliance with this hive, she had to give _something _back after the edge they'd just received.

"We could render assistance," she said, shrugging in a meant-to-be-dismissive manner as she addressed the screen once again.

"_You would do this_?" the Queen asked.

"We're supposed to have an alliance, aren't we?" Elizabeth replied. "Sending information on Wraith technology was a remarkable act of good faith on your part."

"_Your assistance would be... acceptable_," the Queen said, a brief smile on her face before she assumed her previously-established cool stare.

"All right then," Elizabeth said. "We have a deal."

Even if she still wasn't entirely comfortable with what they were planning to do here, she had to admit that the possibility of getting this kind of information about Wraith technology helped her feel significantly more optimistic about the future; maybe they could use what they found here to work out another way of immobilising the Wraith ships without needing to actually _kill_ anyone else by turning them into a new food supply.


	24. On the Road Again

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Mystery of the Phantom

As he crouched in a convenient maintenance tunnel near the centre of the city, his ears alert for the radio transmissions that he'd arranged to be rerouted via his mask if certain key words were heard- he may not know much about creating computer programming, but you didn't spend around two decades in a city like this without learning a few neat tricks-, John had to wonder if the current analysis was turning up anything about the hives that he himself hadn't picked up through trial and error. He might have learned over the years that each hive tended to have a better ability to cope with particular kinds of damage than its fellows, but that didn't mean that there weren't some areas that could be attacked that would do particular damage to the rest of the hive rather than just areas where the hull was particularly weak in one ship compared to how it was in others...

He wondered if it was still normal for him to have concerns about the Wraith even after all they'd done so far to live up to their end of the original deal. They'd even allowed McKay and Ronon to take a look around the hive and let them return to Atlantis afterwards without any objections or any sign that they had any problem with what the two men had seen or done while on the hive; for any Wraith to allow a non-worshipper on a hive like that was a _definite _step in the right direction for this alliance.

Still, their look at the Hive's interior had certainly helped them come up with a neat way of dispersing the retrovirus throughout other hives without worrying about issues of explosive devices igniting the resulting gas. Based on what he'd overheard in his last trip to the conference room as Sumner and McKay spoke to the Queen, McKay had isolated a central chamber that removed the CO2 from the ship's atmosphere that would allow them to disperse the retrovirus throughout the ship so long as they could get a canister of the stuff in there in the first place.

It might not be a perfect plan- as the Wraith Queen had pointed out herself, the only way to get that canister into the chamber that they'd thought of so far was to use the expedition's Asgard transporters to send it there-, but it was a step in the right direction; anything that would limit the threat the Wraith could pose to others was a step in the right direction as far as he was concerned.

He just wished he could figure out what was bothering him about this whole situation; the Wraith hadn't done anything to merit him being _really _suspicious of them apart from the fact that they were Wraith- and he wasn't going to let _that _get to him after his previous 'debate' with Michael-, but there was definitely something about this whole thing that he didn't feel entirely comfortable with yet. He acknowledged that it was probably just his natural disinclination to trust the Wraith after everything they'd driven him to over the years in order to survive, but that experience had also given him a sixth sense for danger that he couldn't afford to overlook just because he found it frustrating.

God, he needed to get _past _this; how was Elizabeth _ever _meant to see him as anything more than a masked vigilante if his response to everything that happened was to wait and prepare for the moment when it would backfire on him-?

Then an alarm suddenly flared up in his ear, followed by one of the emergency systems he'd installed in his mask activating to display a stream of information in his left eye- the small computer he'd installed there could itch at times, but if he was going to 'pad' that section of the mask anyway to make it look natural he was going to install something that served some kind of purpose-, and he knew that his fears were justified.

"_Fuck_..." he muttered to himself, as he closed his right eye to better process what was being displayed in front of his left. "So much for _that _hope."

The Wraith might not have shown any sign of hostile intent so far, but sending them a computer program equipped with a virus that would delete everything they'd sent to Atlantis _and _send the hive a message containing certain items of data wasn't something he wanted to think much about. Acting as quickly as possible, he reached out with his mask's mental sensors and quickly shut down the computer network- the worm had still sent off something, but by taking the computers offline for the moment he should be able to prevent it getting everything that it had been designed to transmit until they could reboot the system and purge it of the virus- before he turned around and began to hurry towards the room where he'd set up his emergency transporter system (He might not be a McKay when it came to gadgets, but he'd come up with _some _interesting adaptations of existing technology in his spare time).

He hated leaving the city while Elizabeth was still on it, but if these events meant anything, it was clear that it was time for him to use one of his 'special projects', and just hope that he'd gotten the programming right (He'd done his best, but when you were working with theoretical programs that the Ancients hadn't even put into practise before they left Atlantis there was only so much you could do) or that he'd have time to make the necessary corrections if this plan didn't work out.

* * *

"What happened?" Elizabeth asked, looking at Zelenka as he sat at her desk, Teyla alongside him out of a lack of anywhere else for her to be at this time, evident shock and terror on his face at the news that he was relaying.

She still wasn't entirely clear on what had happened or why the computers were rebooting right now, but she had a strong feeling that she was about to learn the answer to both questions soon, and she was equally certain that neither of them were going to be entirely pleasant.

"We got hacked," Zelenka said, staring ahead of himself as he spoke, apparently trying to avoid addressing her directly out of fear at her possible reaction. "Within the hive ship's schematics was a worm-like computer virus."

"Your people went over the data," Elizabeth said, trying to trace where the Wraith's deception of them had begun as she walked around to take her seat.

"I know," Zelenka confirmed. "We thought it was clean, but this virus was entirely different."

"What did it do?" Elizabeth asked, taking up position behind her desk as she leant forward slightly while continuing to face the Czech scientist.

"It very selectively probed our systems without damaging them or exposing itself," Zelenka explained.

"I don't understand," Beckett said, voicing Elizabeth's own confusion from his position at the side of the room. "If you didn't find it and it didn't reveal itself..."

"Once the hive left Atlantis," Zelenka clarified in response to Beckett's question, "the worm began to destroy all of the data they had sent down.

"Then this was their plan all along," Teyla said, her grim tone and resigned expression suggesting that she was berating herself for allowing herself even the brief hope that they found a Wraith who wasn't the same as the others.

"What did they get?" Elizabeth asked, hoping that she would be about to hear some good news;

"Well," Zelenka said, smiling slightly as he spoke- the smile faded as he continued to relay the information, but at least it provided Elizabeth with confirmation that _something _had worked out in their favour-, "apparently whatever happened to the computers caused them to shut down mid-transmission- the worm was programmed to activate as it was erasing the information from our databanks-, but from what I was able to see before the computers deactivated, the worm was able to send the Aurora mission reports..."

"And what else?" Elizabeth asked, sitting down in her chair as she noted Zelenka's suddenly apprehensive expression.

"The location of most of the worlds on our database," Zelenka said grimly. "I can't be sure which ones got through before the computers were shut down, but-"

"Doctor Weir!" Chuck's voice suddenly said, the technician hurrying into her office with an expression of obvious confusion on his face. "We have a gateship lifting off from the... well, the underwater gateship bay!"

"The _underwater _one?" Elizabeth asked, turning back to look at the technician in confusion, her mind quickly going over what she remembered of the reports on the submerged gateship bay they'd located underneath Atlantis. "But I thought we hadn't been able to-"

"We _haven't_," Chuck said, looking urgently back at her. "That's why I thought you should know; whoever took the jumper took care not to let us know they were using it until it was actually some distance away from us, and now-"

"_Atlantis, this is Jumper Alpha Omega One_," a familiar voice suddenly said over the now-reactivated radio, sounding almost grimly jocular as it spoke.

"Jo- _Phantom_?" Elizabeth said, quickly reminding herself that she was in public as she activated her radio to respond to this sudden message. "What are you-?"

"_I'm sorry about shutting down the city's computer network like that, but I had limited time available to me after I realised what the Wraith were up to; I had to move quickly if I was going to stop them getting everything they were after, and terminating Atlantis's ability to send that information before it was completed was all that I could think of_," John's voice interrupted, his tone an abrupt professional one that he never used when the two of them were alone. "_Given the contents of the downloaded files, I'm sure you can agree with me that our immediate priority right now should be to prepare for the worst and send _Orion _and _Daedalus _after the hive as soon as possible; I'll do what I can to catch up- following them shouldn't be too difficult; it's just issues like precisely _where _they'll stop that's the problem-, but considering that this thing's a prototype I won't be able to push it as quickly as I'd like_-"

"Hold on; what are you talking about?" Elizabeth asked, trying to get a word in to be sure she understood what her mysterious masked friend was saying to her.

"_The Wraith have acquired the information they need to make their hyperdrives inter-galactic from the _Aurora _files, and at least the hive you've been working with for the past few days- and maybe one or two more- are now on their way to Earth_," John replied, his tone a simple one that left no room open for hesitation or doubt. "_Get in touch with_ Daedalus_ and_ Orion _and send them after the ship as soon as possible; I'll do what I can, but even if I catch up with the hives I'm definitely too small to do that much to them right now_."

"But-" Elizabeth began, before the radio connection suddenly terminated, Chuck turning to look at her in surprise a few moments later.

"The gateship just... went into hyperspace," he said, his confusion clear as he spoke.

"Hyperspace?" Elizabeth repeated, before she turned to look at Zelenka inquiringly; she acknowledged that it was a stupid thing to focus on, but she couldn't do anything about whatever the Wraith had received in that last transmission. "Would that even be possible?"

"With the right modifications to the engine system, I suppose they _could _go into hyperspace, but we have no way of knowing what those modifications would be; analysing the possibility of adapting the gateships for hyperspace hasn't come up so far-" Zelenka began.

"Atlantis_, this is _Daedalus," Colonel Caldwell's voice suddenly said over the radio, the transmission cutting off Zelenka's explanation. "_Our hive-ship turned on us- along with the hive we were planning to test the retrovirus on- and then they both jumped into hyperspace before we could do much damage to them in return_."

Elizabeth's blood ran cold, all thoughts of what John might have done to that gateship forgotten.

She didn't need to be a diplomat to know that, in a situation like this, it was what _wasn't _said that mattered almost more than what was said.

"Where are Doctor McKay and Ronon Dex?" she asked.

"_They were still on the hive-ship when it went into hyperspace_," Sumner's voice said, answering Elizabeth's next question before she'd even asked it; at least _he _was still here, even if she would have preferred John to be at Atlantis if she'd had a choice between the two of them. "_We're on our way back to Atlantis with injured, but_-"

"We already know where they're going," Elizabeth said, her voice grim as she exchanged brief glances with Chuck and Zelenka before she continued, recognising from their lack of objection that they understood and agreed with what she was about to do. "They were apparently able to transfer a virus into our systems when they gave us the information on their ships earlier; this virus allowed them to download the information we acquired during the _Aurora _mission, which we believe they've used to upgrade their hyperdrives to inter-galactic, and we have reason to believe that they're on their way to Earth."

"_Earth_?" Sumner repeated, shock clear over the connection before he continued speaking again, this time in a more professional tone. "_Have Major Lorne prepare_ Orion_ to pursue and engage those hives as soon as we get back; the crew are doing what they can here, but it's unlikely that _Daedalus _will be in any position to begin pursuit immediately after the damage we took here_."

"Understood," Elizabeth said in response. "I'll see you when you get back."

She didn't need to look at the other people in the control room as she terminated the connection to know that they were thinking the same thing as her; in this kind of situation, _Daedalus_'s condition almost didn't matter.

As powerful as _Orion _was, it was still only one ship in an ambiguous state of repair- they had most of the systems up and running, but they had no way of really knowing how many crew were needed for it to operate at its peak- up against two Wraith vessels at full strength; nobody could be blamed for her wanting to ensure that _Orion _wasn't alone in its upcoming fight, particularly not with the current stakes facing them.

After she received the news that _Daedalus _had landed and reapirs had already begun on the damaged ship, Elizabeth wished that she could think of any kind of alternative course of action beyond the one that she was committed to at the moment; the idea of ordering people to what would probably be their deaths just to be sure was something she'd _never _wanted to resort to...

But, in the end, she also knew that she didn't have a choice; even if she'd received this command because some politicians wanted to 'play nice' with each other, John had been right when he'd told her that she wouldn't have kept this job if the right people didn't think she could still do it.

She might not be a military commander, but she was the leader of the colony that Earth had established on Atlantis, and she was going to fulfil that responsibility, no matter how distasteful she might find it.

* * *

"Colonel Caldwell, Colonel Sumner," Elizabeth said, looking over at the _Daedalus _and Atlantis military commanders as they walked up the rear stairs into the control room. "What's the status of the repairs?"

"Ongoing," Caldwell said, nodding grimly in response to her question, clearly deeply affected by recent events. "We lost a few key personnel in the attack."

Elizabeth wished that her primary emotion at that news wasn't relief that so far nobody she knew well had died; as a leader, she naturally felt responsible for every death that took place in Pegasus as a result of her decisions, but that didn't mean that she wasn't allowed to grieve for some deaths more than others.

"I'm sorry," she said, hoping that this apology would be enough as she turned to lead the way into her office, Caldwell, Sumner and Teyla close behind her as Zelenka joined them.

"I wish we had the time to mourn our losses, but the fact is that we don't," she said, walking into her office and taking up position behind her desk, grateful for Teyla's presence alongside her as she spoke; even if they weren't as close as she might like, she still considered the Athosian a close friend, and she needed that kind of reassurance at a time like this. "I just briefed General Landry. We're to check in in an hour and advise him of our response to this."

"I can have _Orion _ready to go in an hour or so- according to McKay's last report the last bits of programming had been written, and new power regulators and all other necessary systems have been installed-, but _Daedalus _won't be able to muster up much of a response-" Sumner began.

"I want you to redeploy both ships immediately," Elizabeth interjected before she could give herself any time to question the decision that she had just made.

She wasn't sure if it should be seen as a good thing or a bad thing that she thought of John when she gave that order; she was trying to act the way he would act in a situation like this, but whether it would have any effect was another matter.

"Excuse me?" Caldwell said, eliminating Elizabeth's hope that she could do this the easy way. "_Both _ships? You want me to send _Daedalus _out as well?"

"So long as they're still in striking distance, we have to at least try," Elizabeth said, keeping her tone solemn and level; raising her voice would encourage arguments, but she'd learned long ago that staying focused while speaking had a better chance of accomplishing her goal through sheer intensity of will.

"You know we can't intercept them in hyperspace," Caldwell said, a slightly incredulous tone in his voice at what he was being asked to do.

"Doctor Zelenka?" Elizabeth said, looking over at the Czech scientist to answer that particular question.

"Well," Zelenka began, "obviously they've upgraded their FTL drives using the information they were able to steal from our database- the Aurora mission reports-"

"Obviously," Sumner interjected, glaring briefly at the scientist, clearly hoping he'd get to the point (Not that Elizabeth could blame him; when Zelenka had first mentioned a means of tracking the Wraith, she'd been as eager for him to explain what he meant as anyone, even if she was slightly ashamed to admit that she'd been grateful for the news that she would be able to help John).

"However," Zelenka continued, as though he'd been about to move on to this topic on his own, "the ships _are_ organic in nature; they _will _need to make brief pauses to recover from the effects of hyperspace radiation."

"Where and when?" Elizabeth asked, even as she mentally noted that this explained John's comment about knowing where they were going to stop; he must have some idea about what kind of stresses Wraith ships could endure from previous encounters with them (She momentarily wondered why he hadn't mentioned it, but dismissed that thought quickly enough; it wasn't like that kind of information would have ever been useful to them before now, so there would have been no reason for John to bring it up).

"Uh, yeah," Zelenka said, slightly shaking his head as he went over the possibility in his mind before he shrugged slightly. "It will take some time to calculate."

"Go," Elizabeth said, nodding grimly at the scientist, Zelenka simply nodding in confirmation before he turned around and walked out of the room (Elizabeth supposed that they should be grateful that the Wraith were heading to Earth; at least they were likely to simply follow _Daedalus_'s usual route to and from the Milky Way galaxy- something about those 'Langara points' that McKay had told her about when they'd first discovered that satellite affecting the gravity in space meant that there were only a certain number of routes you could take to reach certain locations-, thus limiting the areas where they might decide to stop).

"Look, Doctor Weir," Caldwell said, looking back at her as Zelenka headed off to his lab, "I want to go after these bastards as much as you do, but the _Daedalus_ is in no position to fight right now. Our shields are severely depleted and several decks are inaccessible; even if we _could_ catch up with them, I don't know how long we'd last."

"Which is why I'm committing the _Orion _as well," Elizabeth began.

"Then why even _bother _with _Daedalus_?" Caldwell asked, still staring intently at her. "From what Marshall's told me, _Orion_'s in excellent shape-"

"It's still not been tested in combat; regardless of the quality of the repairs that the Taranians and the Phantom have performed on it before we got a chance to work on it ourselves, I don't want us relying exclusively on a single ship when faced with stakes like this," Elizabeth interjected, staring grimly at Sumner and Caldwell, relieved to see Sumner nodding slightly at her assessment of the situation; he might not be happy with her decision, but at least he could appreciate why she had made it. "You've got some time until Doctor Zelenka can finish his calculations to deal with the worst of the damage right now; anything else you should be able to handle on-route."

"And if we can't?" Sumner asked

"Currently," she said, walking out from behind the desk to look more directly at the two colonels, her face betraying no sign of whatever personal reasons she might have for ordering them on this particular mission, "Stargate Command has no vessels capable of engaging the hive ships before they reach Earth. They _cannot_ be allowed to get that far, Colonel."

For a moment, Caldwell simply stared at her, swallowing as he briefly looked away, exchanging brief glances with his Atlantis counterpart before he stared back at her.

"You're aware that there's a good chance this won't end well," he said at last.

"I am," Elizabeth replied, wondering as she spoke why the silver face of a masked man with some unspecified injury underneath that mask was the first thing that came to mind when he mentioned that; she was actually _ordering _Caldwell and Sumner to mount what could be considered a suicide mission, she should be worried about _them_...

"There's still repairs that need to be made," Caldwell said after another contemplative pause, glancing briefly over at Sumner. "Can I-?"

"Everything we can spare is at your disposal," Sumner confirmed.

"Do what you have to do," Elizabeth said, offering her own support for the two men as Caldwell and Sumner walked away, leaving Elizabeth to exchange grim glances with Teyla as she processed what had just happened.

She might have Sumner's support regarding her recent decision- or at least she didn't have his opposition; where Sumner was concerned the two amounted to basically the same thing in her experience-, but that didn't mean she was happy about it; she hadn't even realised how much she'd come to depend on John's faith until he wasn't here to give it to her.

It wasn't that she couldn't make decisions without him- their argument over Michael proved that-, but she would have just felt happier if he'd been there to talk to; the simplicity of the faith he'd always had in her always helped her feel... better about herself, somehow.

Right now, however, all that she could do was wait and hope that, wherever John was, he knew what he was doing; if Caldwell and Sumner couldn't get their only two available ships ready in time, the man who'd defended the Pegasus Galaxy for the last decade or so could be Earth's last hope.

As much as she believed in John- to a point where even she was surprised at the extent of the faith she had in him-, there was only so much one gateship could do against _two _Hives...


	25. Alliances in Shades of Grey

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Mystery of the Phantom

"_Dammit_!" John muttered, anxiously thumping the jumper's controls as they sparked again; he'd known that this thing was going to have some trouble coping with these speeds, but he didn't think it was going to be _this _bad. He supposed that it was his own fault for not going with the ZPM-powered option, but it wasn't like he'd had much choice; without the ability to manufacture more of those things, he wasn't going to waste one of the relative few he'd managed to collect to power something that could function fairly well on its own.

He just wished that he had a better plan for what he was going to do whenever he managed to catch up with the Hive. Based on the transmission he'd intercepted from the _Daedalus _as he departed Atlantis- he'd reverted back to normal space after leaving Atlantis's immediate sensor range to keep an ear out for anything from _Daedalus _and had lucked out by intercepting the subsequent transmission-, he should only have to worry about a couple of Hives, but even that was a fairly significant amount to worry about considering the relatively limited resources he had available to him right now and their own exceptional size.

He might not be able to destroy either ship with his current supply drone weapons, but if he could just find the right area to shoot at, it might still be possible for him to disable the ships long enough to increase the possibility that Atlantis would be able to send back-up before the Hives reached the danger zone...

Whatever the case, he had to at least try and fight them; he'd become the Phantom to protect Earth from this kind of threat, and he wouldn't give up just because it was going to be more difficult to pull this off than it would be for him to try this kind of thing normally.

* * *

As she sat in Atlantis's control room, staring at the screen that was currently relaying her image to Earth while allowing General Landry to respond in kind, Elizabeth couldn't help but feel a slight thrill at the thought of the long-distance call they were making.

It might be a slight drain on the ZPM to even do this much- the ZPM that had been connected to Atlantis when they arrived was on its metaphorical last legs, although the fresh one SG-1 had recovered in Egypt still had a significant amount of power left in it despite that-, but the idea that they had reached a point where they could stay in touch with people on the other side of the galaxy in a matter of moments was one of the many miracles that they'd uncovered since coming to this city; the sheer range of possibilities this city could provide them with still amazed her...

"In approximately one hour, the Wraith will drop out of hyperspace... here," she explained, pushing a button to bring up a star map on the side of the screen even as she continued to address General Landry (She might have privately preferred General O'Neill as a commander for the SGC given his superior understanding of the galactic situation from out in the field rather than Landry's report-based knowledge, but she had to admit that the other general wasn't a bad alternative) and Sergeant Harriman on the screen. "It's just outside of the Pegasus galaxy. There, they will pause for fifteen hours. If _Daedalus_ and _Orion_break orbit on our current schedule, they should be able to reach those coordinates in around thirteen or fourteen hours, best possible speed."

"_A narrow window_," Landry noted grimly.

"It's the _only_ window, sir," Elizabeth replied, deciding not to mention that it was a window that was partly possible thanks to the Phantom's work with the Taranians; if he hadn't assisted them in carrying out at least some of the repairs on the _Orion_, then it was unlikely that the Atlantis expedition would have managed to get the hyperdrive or the weapons up to working order in the time available to them.

"_Understood_," Landry replied. "_Now, the International Oversight Advisory want you to brief them on this matter_."

"When would you like me to dial in again?" Elizabeth asked, already planning the report she'd have to write; if she focused, she could probably get the job done in a couple of hours...

"_You misunderstand me_," Landry said, looking at her with an earnest honesty that made it clear he wasn't joking. "_I mean in person, and I mean right now. The President himself assigned_-"

"I can't just leave," Elizabeth interjected, shaking her head; with John, Sumner, McKay and Ronon absent, Atlantis was already short far too many of its senior personnel for her taste (Not that she'd ever admit to the fact that she thought of John as a senior member of the expedition; the last thing she wanted was to give anyone _that _kind of potential ammunition against her). "Not now."

"_I'm afraid that's not up to you_," Landry said, shrugging slightly.

"There is far too much going on here-" Elizabeth began, trying to convey the current urgency of the situation to the general.

"_Doctor_," Landry interrupted, before his voice softened as he continued to speak. "_You've done all you're going to do for now. I need you to step through that Gate. They're waiting for you in my Briefing Room_."

Elizabeth couldn't believe it; after all the effort she'd put into trying to arrange a defence against the Wraith- to say nothing of everything that she was putting at risk to try and stop them completing their mission- the IOA were _still _more focused on pointing fingers than acknowledging that she was trying to correct the 'mistake' that she'd made with the full support of them and her staff...

"_Doctor Weir_?" Landry said, breaking her train of thought as he looked curiously at her.

"I see," Elizabeth said at last, grateful when Landry at least smiled sympathetically at her. Nodding back at him in response, she turned and picked up a laptop computer from a nearby console before she stood up and turned to Teyla.

"Teyla," she said, trying to focus on the immediate issues that the Athosian would have to deal with in her absence, "we are awaiting several teams to return from their missions. Once that happens, I'd like to suspend all Gate travel until this whole thing is over."

"Of course," the Athosian woman said; Sumner might occasionally express doubts about Teyla's abilities in this area, but Elizabeth was confident that her friend could handle what she was up against.

Turning to look at the screen showing General Landry for a moment, Elizabeth looked around the control room, hoping that this wouldn't be the last time she had a chance to look at it, before turning back to Teyla.

"And I'll need you to dial in once the _Daedalus_ is ready," she added, indicating Atlantis's DHD.

"I know what to do, Elizabeth," Teyla said, smiling in reassuring understanding at her.

"Of course you do," Elizabeth replied, smiling awkwardly.

"I will see you when you return," Teyla said, the Athosian's simple confidence in that outcome helping to improve Elizabeth's mood despite the current personnel shortage.

"Thank you," Elizabeth said, exchanging smiles with Teyla before she walked away, leaving Teyla to sit down at a console as Elizabeth walked down to the gateroom (She'd worry about getting her things sent to her later; from what Landry had said, there wasn't going to be any time to pack if she wanted to avoid getting in even more trouble with the IOA) and through the Stargate...

* * *

Emerging from the Stargate into the SGC- she wondered if it was just her time with John that had left her feeling that a trip like that should feel more dramatic rather than simply feeling longer-, Elizabeth barely had time to take in her surroundings before she noticed the general standing at the end of the ramp.

"Welcome back to Earth," Landry said, smiling at her.

"Thank you, General," Elizabeth replied, not even bothering to fully restrain her sarcasm as the Stargate shut down behind her; it might be one of John's more troublesome personality traits, but if she'd learned anything from him it was that she shouldn't allow other people to see how afraid she was. "It's wonderful to be here."

"I can see that!" Landry said, his own good mood alleviating her bleaker one slightly as they turned to walk out of the Gateroom while the security teams dispersed around her.

"You know I considered disobeying your order?" Elizabeth said, briefly reflecting on how far she'd come since her original days in the city when she would have tried to be more polite when arguing about decisions she didn't fully agree with. "There wouldn't have been too much you could do about it."

"You made the right decision in coming," Landry replied, ignoring the implied threat.

"We're in the middle of a crisis, General," Elizabeth countered. "This is absolutely-"

"Don't bite _my_head off, Elizabeth!" Landry interjected, looking pointedly back at her. "The recall order didn't come from me."

"Who it came from doesn't matter," Elizabeth said.

"What if I told you it came from the President?" Landry responded.

"I wouldn't believe you," Elizabeth replied, considering and discarding that possibility immediately; whatever other problems she might face at this time, she was fairly sure that Hayes and General O'Neill still supported her current position.

"And you'd be right," Landry said, as Elizabeth walked over to study the monitors displaying the location where they'd calculated the Wraith hives would pause to 'recharge'. "But in a couple of weeks, there could be aliens on our doorstep determined to feed on the human race. The President had no choice but to accede to the I.O.A.'s demand that you be brought back to explain yourself."

If there was anything that Elizabeth regretted about getting back in touch with Earth, it was the reminder that she was no longer the top of the proverbial food chain when it came to making decisions that might affect Atlantis.

It wasn't that she was arrogant enough to think that she'd always make the best choice if she was the only person she had to answer to; she just wished that she could be judged for her actions by people who knew what it was like out in Pegasus, rather than people who were always looking to secure their own position even if it came at the cost of someone else's.

"So what do they _really _want?" she asked, glancing up at the briefing room at the top of the stairs at the back of the control room.

"To point fingers, and cover their asses," Landry said, confirming Elizabeth's lowest expectations of the reason for her presence here.

"I am honestly not sure how I will respond to _that_, sir," Elizabeth replied, her voice low with the same slightly threatening edge that she'd picked up from John during his talk with Kolya.

"They're bureaucrats, Elizabeth," Landry replied, a smile back on his face as he spoke. "You'll have 'em for breakfast!"

Elizabeth wondered if she should feel encouraged at that compliment or simply feel frustrated at the apparently pointless reasons for the IOA to call her back in the first place; the world was facing destruction, and while Sumner, Caldwell and John were trying to save it, the IOA were focused on making sure that she took the blame for something that she'd only done because _they _had allowed her to go that far.

This was definitely one of those occasions where she could see the merit in John's usual approach to dealing with his enemies; it might be brutal, but at least you didn't have to worry about them constantly bothering you...

_God_, she hoped he was still alive.

* * *

As John came out of hyperspace on the outskirts of Pegasus, he allowed himself a relieved smile at the sight in front of him; the two Hive-ships, resting on the edge of their home galaxy, out of hyperspace and preparing for the next jump.

Actually, given that the ships themselves were living organisms, he was put in mind of the idea that they were simply hesitant about leaving their natural environment for unfamiliar territory; it might not be a completely accurate description of the situation, but he felt that he was entitled to consider things in an overly melodramatic manner considering the stakes that he was up against.

Two whole hives and all he had was a few drone weapons; even if he tried to mount a kamikaze assault by using the jumper as a weapon after he'd used his drones on one hive, there was no guarantee he'd take out both of them without getting blown up himself...

_Still_, he reflected to himself, smiling slightly as he reached up to activate his mask's recently-installed radio, _since I _might _have back-up on board, best to establish its presence as soon as possible_...

"Doctor McKay, Specialist Dex, are you there?" he asked; this gambit might be risky, but if Dex and McKay _were _on board, their combat and technical expertise might just make them two of the best people qualified to help him in this current mess. "I know that this is a long shot, but if you can hear me, please respond; I need to know if anyone's alive on one of those things I need to worry about saving..."

"_Phantom_," an initially unfamiliar voice said over the radio, a slightly apprehensive tone to its voice. "_Is that you_?"

"Who's this?" John asked; he thought he recognised the voice, but it _couldn't _be that guy.

"_You know me as Michael_," the voice replied.

John couldn't help but sit in silent surprise for a few moments; whatever he'd been expecting to hear, a reunion with Michael- even one that just took place over the radio- was _not _something he'd been planning for...

"And what do _you _want?" he asked, not bothering to try and avoid the current topic; they'd already started talking, so he was pretty much committed to his current course of action now.

"_Among other things, you may appreciate knowing that Ronon Dex and Doctor McKay are still alive_," Michael responded.

"What are you going to do with them?" John asked, forcing down the brief shred of hope he felt as this implication that Michael wasn't your average Wraith; he'd given the guy _one _chance and he'd basically gotten kicked in the teeth for even offering it...

"_If you want them to live, listen to me_," Michael replied grimly. "_I don't know how you got aboard, but if your would-be allies from Atlantis are in pursuit, you need to disable these ships in order for them to reach us_."

"If you're trying to help us, why don't _you _do that?" John countered, resisting the temptation to clarify that he wasn't part of Atlantis's command structure; this was far from the time or place to have debates about the specific nature of his role in the expedition.

"_They would know_," Michael replied grimly.

"What happened to you being one of 'them'?" John asked, even if he already knew that he wasn't sure what answer he wanted to receive in response to that question.

"_Please believe me when I say I was as deceived as you were_," Michael said, his tone becoming increasingly urgent, lending some weight to the idea that he was worried about being discovered even if John remained unconvinced.

"I always had my _slight _suspicions- it's why the download was cut short before it could be completely finished-, but why are they acting against you?" John asked, refusing to get his hopes up; the stakes were too high for Michael to trick him...

"_It seems, Phantom_," Michael replied, "_that because of what your allies did to me, the Wraith no longer see me as one of their own_."

"Ah," John said, forcing down the slight disappointment he felt at the news that Michael's 'defection' was motivated by necessity rather than choice. "So you want to help me just because you don't feel welcome there any more."

"_We don't have time to discuss this_," Michael said rapidly. "_Where are you_?"

"Just off to the side and coming in from a distance under cloak," John replied; it was vague enough to avoid giving anyone any way to track him if this was all a trick of some kind, while at the same time being potentially useful if Michael was genuinely trying to help him. "Why do you ask?"

"_If you target the ventral hyperdrive generators, you will cause the most effective amount of damage_," Michael replied, confirming John's initial plan while also confirming that alternatives might not do any good.

"You're sure this isn't some screwy trap?" John asked, trying to focus on the main issues.

"_I doubt I'll be allowed to live much longer, and yet I very much want to continue living_," Michael said, his tone still grim as he spoke. "_If you want to survive as I do, then I suggest you go along with my suggestion_."

John didn't bother replying to that suggestion as he turned off the radio and focused his attention on the relevant problem of getting into the right position for his next attack.

If he opened fire too early, there was still a good chance that he'd damage the wrong part and trigger a chain reaction that would end up destroying the ship with Ronon and McKay still on board; all he really wanted right now was something to damage the engines without having too great a knock-on effect on the Hive's _other _systems...

_Great_, he reflected grimly, even as he moved the jumper into position. _My first major op in two years, and I've got to rescue the hostages while relying on a guy who has no reason _not _to stab me in the back_.

Wanting to believe Michael didn't mean that he _could _believe him; even if this plan resulted in the generators being disabled long enough to give Atlantis or Earth time to send other ships here, he still had to get past such issues as how he was going to get on board to rescue McKay and Ronon before everything went to Hell...


	26. Breaking Into Hives

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Hope nobody minds about my timing decisions here; later events in the battle against the Hives might be a bit quick, but I think what I've got works in the context of the original episodes

Mystery of the Phantom

As she sat opposite the IOA representatives assigned to question her about the recent turn of events in Atlantis, Elizabeth wondered once again who in the world had thought that putting these people in a position of even indirect control over the SGC had been a good idea after all the trouble that ex-Senator Kinsey had caused during his time in office; looking over the files, she was amazed that more people hadn't seen sense after Kinsey's decision to try and shut the program down would have led to Apophis destroying or conquering Earth if SG-1 hadn't defied orders. The creation of the IOA might have convinced the Pentagon to approve the SGC's renewed budget after the Ori and the Wraith were confirmed as a valid threat, but that still left them with various bureaucratic idiots with a position of authority to permit or terminate any project that the SGC or Atlantis might want to carry out, regardless of the recommendations of the military and scientific forces who actually had first-hand knowledge of what they were dealing with.

She might have been one of them back when she'd started in the program to an extent- the idea that her younger self still thought that it had been a good idea to negotiate with the Goa'uld could still shock her at times-, but at least she'd had enough intelligence to recognise when she should delegate to the wisdom of Colonel O'Neill and the rest of SG-1 rather than ask them to follow her or Kinsey's orders just because they were SG-1's official superiors.

"The leader of the Hive presented a scenario which made it seem we were under a time constraint," she explained, putting her thoughts to the side as she looked between Woolsey, Shen, and the British ambassador whose name she hadn't registered. "To speed up the problem-solving, we distributed the file-"

"And played right into their hands," Shen said, with a cold, smug voice that suggested that she would have seen through such a deception (If it wasn't for the fact that she'd probably destroy something before she learned her lesson, Elizabeth would like to see how Shen handled being the one having to make the decisions that she faced on a regular basis for a change).

"...Yes," Elizabeth admitted after a moment's pause, unable to find a better way to reply to that statement without saying something she'd professionally regret.

"In fairness," Woolsey added, leaning forward slightly as he looked at Shen, "Doctor Weir kept us informed of every action they took along the way."

"And we supported her recommendations, I know," Shen said, briefly looking at Woolsey before turning back to face Elizabeth. "But clearly we were not in possession of all the facts."

"Obviously, neither were we, Ambassador," Elizabeth retorted, resenting the implication that she might have kept something back. She might be regularly 'bending the truth' when it came to her interactions with John- as far as the rest of the Stargate program was concerned, he showed up now and again and vanished until the next crisis that required his assistance took place-, but that was the _only _thing she was lying about on an even semi-regular basis.

"So what measures have you taken to prevent the Wraith from reaching Earth?" Woolsey asked, as Shen sat back slightly in her chair.

"I was coordinating a strike against the hive ships when you recalled me," Elizabeth retorted, already making up her mind to avoid mentioning the Phantom unless she had to; she didn't know what John was precisely going to do when he reached his destination, and she doubted that the IOA would have that much patience for her apparent reliance on a 'vigilante' no matter how reliable he'd proven himself to be so far.

"With what?" the English ambassador asked uncertainly.

"With everything we've got," Elizabeth replied, hoping that the cold resolution in her tone would stop any further questions being asked.

"Is that wise?" Shen asked.

"General Landry has informed me that in light of fleet resources committed to fighting the Ori, the weapons platform in Antarctica, powered by a pair of Mark Two generators, would be Earth's only defence," Elizabeth countered, staring between the three people before her as she spoke. "Now, I believe it would be _far_ better to stop them while they're still within reach of Atlantis."

"Wouldn't it have been more prudent to send the ZPM back to Earth on the _Daedalus_, ensuring successful operation of the Antarctic weapons platform when the Wraith arrive?" Woolsey asked, instantly ruining the slight hope Elizabeth had formed that she had an ally in him after his earlier defence.

"The _Daedalus_ suffered severe damage during the first battle," Elizabeth replied, already knowing that this new information wouldn't go down well. "A long journey at full power was out of the question... and there is no way of knowing how much faster the Wraith ships have become."

"You would risk the lives of everyone aboard those ships in order to undo your mistake?" Shen asked; only Woolsey's obvious discomfort at that allegation prevented Elizabeth from taking a page out of John's book and punching the other woman (He might be a violent influence, but there was definitely something satisfying about his method of solving problems).

"I would ask them to risk their lives to protect Earth from a threat that we have _all _accidentally unleashed on Earth due to our desperation to defeat the Wraith blinding us to the fact that we were all deceived," Elizabeth retorted; she had spent too much time witnessing John in action or thinking about him not to have picked up some idea of how he coped when under this kind of pressure, and one thing John always was in a crisis was direct. "_Daedalus _is currently undergoing emergency repairs over Atlantis and will be prepared to break orbit in the next hour; if you want to call back and order them to take the ZPM back to Earth instead, you can feel free to do so, but you need to do it immediately."

"Then, if you'll excuse us, we need time to discuss our options," the English ambassador said, his uncertain tone as he looked at the other two confirming Elizabeth's lowest expectations for the current meeting; as always, nobody here would do anything for fear of being blamed if it went wrong.

"I have instructed Atlantis to contact the SGC when both _Daedalus_ and _Orion_ are ready to leave," Elizabeth said, standing up as she looked confidently between the IOA representatives in front of her, resolute in the knowledge that none of them would be able to effectively defy her without getting into the very position they wanted to avoid. "If you would like to overturn my standing orders at that time, go right ahead, but you will have to fire me first."

She might not agree with the political games that she had to play right now, but she at least knew enough about the way these peoples' minds worked to know that she'd just given them the perfect ultimatum; she'd put them in a position where their only option was to go along with her current plan or they'd have to actually take personal responsibility for something.

All she had to do now was wait for Atlantis to get back in touch with her, and hope that John had a plan to delay the Wraith long enough for _Daedalus_ and _Orion _to get to the Hives in time to take them out; _Orion _might be powerful and in relatively good condition, but it was still relatively untested in combat.

Their current plan might just consist of getting to the Wraith ships- and that counted on them making various suppositions that might not even be accurate- and hitting them with everything that _Daedalus _and _Orion _had to offer, but she _had _to hope that John had something else up his sleeve...

* * *

As he sat silently in his hyperspace jumper, grimly going over the various details of his current 'plan'- he knew that he had taken his time to prepare, but the closer the Wraith were to returning to hyperspace the more damage he'd do; if they had to start repair work all over again, so much the better-, John just hoped that he wasn't making too many assumptions right now; this situation might be unprecedented, but he _really _didn't want to find out the hard way that he'd made any faulty guesses.

One slip-up if this plan went wrong or he targeted the wrong area, and there was a good chance that he'd kill McKay and Ronon before any help that Atlantis was going to send could reach them, and he'd have _definitely _killed himself (Michael was more of an ambivalent ally at the moment, so John wasn't that bothered about what would happen to him in that scenario; he might be helping John right now, but even the most optimistic part of John couldn't shake the warning that Michael was only doing this to save his own neck)...

"You're sure that McKay and Ronon are nowhere near the area I'm meant to attack?" he asked, as he prepared himself for what he was about to attempt; blowing up Hives was one thing, but he'd never been in a position where he was trying to damage a Hive without _destroying _it.

God, things had been simpler when he didn't have to worry about other individuals...

"_I'm certain_," Michael replied, only a slight edge of apprehension in his voice to indicate the sincerity of his words. "_Good luck_."

"On the topic of location," John said, deciding that he might as well make sure that his current plan was as resolved as he could accomplish right now, "get to an area near the dart bay on your hive-ship; I'm taking out those ventral hyperdrive generators, and then I'm coming in."

"_You are... what_?" Michael asked, clearly unable to believe what he'd just heard.

"Coming in," John repeated grimly. "Look, I'm not going to blow up those ships _completely_ while McKay, Ronon and you are on board, and right now you're the only person I'm in contact with, so I need you to get whatever equipment was taken from them earlier and move to somewhere near the dart bay so that I can pick you up and then try and find them before things get ugly."

He paused for a moment before he continued speaking. "Just to confirm, firing at the ventral generators won't _destroy _these Hives, right?"

"_They will cause damage, but the Hives themselves shall remain intact; unless you possess any weapons of sufficient size to cause the necessary damage, I would recommend you restrict your ambitions for the moment_," Michael said, a slightly grim tone to his voice as he spoke.

"My 'ambitions' right now just focus on keeping these ships busy long enough for me to rescue you and for the big guns to get here; as I said, I'm not going to blow those ships up while you're still on board," John said, glaring for a moment despite the relatively useless nature of the gesture over a radio communication before he continued. "Now, get into position and let me do my damn job."

"_Understood_," Michael said after a brief pause, sounding slightly confused about what John was actually planning to do even if he recognised that choices were limited. "_I will be near the 'dart' bay soon; I will send you a signal when I see you arrive_."

"Good," John said, tightening his grip on the jumper controls. "You might want to hang on to something; when I start firing, this is going to be bumpy."

As he terminated the radio link, John swung the ship around and moved into position behind the Hive ships, quickly targeting his ship's six available drone weapons on to the relevant targets; it might not be _quite _enough to do the kind of damage he'd prefer to achieve right now, but with the ship's armament what it was he'd just have to make do with what he had. Aligning the targeting system as he took up position underneath the Hives, John aimed the drones at the ventral generators- fortunately the two ships were pretty much side-by-side and close together; given how quickly the drones moved he didn't really need that much time to move into position, but given how fast Wraith darts could be the less time the Wraith had to intercept the better-, decloaked, and fired his weapons, watching in satisfaction as the generators on the lower left side of both hives exploded with a force that would have annihilated at least a few blocks back on Earth

"Target is destroyed," he said, turning the ship around to face the now-opening dart bays. "I'm initiating radio silence; see you inside."

With that, he terminated the radio connection- if Michael wasn't going to get into position now then he wasn't going to do anything- and turned his attention back to the space in front of him, the Darts already departing from the bays to search for the source of their recent attack.

Giving them a few seconds to observe his presence, John activated the cloak and began to quickly head towards the bay of the ship that Michael's signal had originated from, swiftly weaving his way through the approaching darts before he slipped into the dart-bay entrance. The narrow tunnel made it difficult to avoid the darts, but John had practised enough at piloting the jumpers to neatly avoid the darts without giving away any other indications of his presence.

After a few moments, he found himself in the main bay, now virtually deserted after the other darts had left to look for him, leaving him free to deactivate the cloak and wait a few moments for the ship's sensors to detect the signal that Michael had transmitted. Turning to follow the signal, John quickly took the ship down to the necessary passage, landing and opening the rear door to allow Michael into the ship.

"Efficient work," Michael said, nodding briefly at him as he sat down in the co-pilot's seat alongside him.

"I'm good at what I do," John said, ignoring Michael's observations of the jumper around him- it was a totally new ship to the guy; it was only _natural _that he'd be curious, so long as he confined himself to looking rather than touching- as he turned his attention back to the jumper, turning it around and bringing up a map of the hive ship's internal layout on the HUD before he spoke to Michael again. "Now, if I wanted to find Ronon and McKay, where would they be?"

"What?" Michael said, looking sharply at the masked man. "Are you-?"

"What I'm planning isn't important to you right now; what's _relevant _is if you can tell me what I need to know to pull it off," John said, glaring over at Michael. "I don't like repeating myself when we're in a crisis like this; where are they?"

"They were kept around... here..." Michael said at last, indicating a particular part of the hive.

"Right," John said, tapping a few additional controls as he re-tuned the ship's sensors to track McKay and Ronon's subcutaneous transmitters- he knew that he wasn't meant to have that kind of information, but it wasn't like the signals weren't available in Atlantis's databanks if you knew where to look-, quickly finding them a short distance away from the location that Michael had identified, a few levels down and a few hundred metres along from their current position.

"What-?" Michael began.

"Hang on," John said, retracting the jumper's drive pods and shifting control to its more basic thrusters- it sacrificed a significant amount of speed, but considering the cramped conditions he was about to try and manoeuvre through and the fact that the ship was still fairly fast without them he thought the trade-off was worth it- as he shifted what power he could to the ship's shields. "This is going to get a bit rough."

What he was about to do was probably certifiably insane, but it wasn't like he had much alternatives available to him right now; with _Daedalus _and _Orion _almost certainly preparing to follow them, he couldn't afford to waste time running through the hive ship on his own to find McKay and Ronon, so he'd have to take the quickest mode of transport available to him and hope for the best.

"Oh no..." Michael said, his voice low and incredulous as John set the jumper in motion and began to fly down the corridor into the heart of the hive-ship, the jumper's exterior scraping the walls on occasion even as he continued his relentless charge through the ship. "You cannot be _serious_..."

"Shut up and let me _focus_, will you; I somehow doubt you want me to crash this thing into a wall because I wasn't _paying attention_!" John yelled, putting the jumper into a tight spin as he spoke, simultaneously lowering the inertial dampers just enough for Michael to feel a slight jolt as he did so in order to ensure that the other guy understood the danger of what he was trying to do.

To Michael's credit, he remained silent for the rest of their 'flight' as John charged through the ship, scratching the walls on occasion until he reached a wider area that Michael barely had time to recognise as the Queen's throneroom before the ship had risen upwards and turned its nose to hurtle down towards the floor. The Hive's exterior might be capable of withstanding drone weapons, but evidently nobody had ever anticipated someone doing this kind of thing _inside _the ship; tearing through the floor like it was paper, John diverted all available power to the gateship's shields as he focused his attention back to the map that he'd pulled up earlier.

Noting that he'd reached the floor where McKay and Ronon were located- fortunately they hadn't moved from the original floor; now that he thought about it, he'd never really seen much in the way of stairs in this ship-, he halted his descent and sent the gateship flying through the nearest corridor, weaving through another series of tunnels until he finally hit the jumper's breaks as he reached the corridor where the scanners indicated that McKay and Ronon currently were (They must have broken out of their original containment cells, although he wouldn't care to guess how long that had taken; he still didn't really know what Ronon was capable of, after all).

"What the _HELL_-!" McKay's voice said, audible even through the jumper's viewscreen as he and Ronon stared at the ship only a short distance away from them, the Canadian scientist's eyes wide with shock.

"Good to see you too," John said, casually activating the jumper's radio system to address the two men as he lowered the rear window. "Now, could you get inside, please? I don't know how much longer we've got before the Wraith realise what I've done, and it's possible that your allies are coming after this lot, in which case I'd like to leave _before _they start to open fire on these ships."

Exchanging brief glances with each other, McKay and Ronon hurried around to the back of the jumper and clambered in, only to halt

"What the _Hell_-?" McKay began to say once again, as Ronon dived for his gun as it lay on one of the benches in the rear and aimed it at Michael.

"He gave me directions; it's a long story," John said, turning around in his chair to glare resolutely at McKay and Ronon, his hand hovering under his cloak to draw his own weapon in case he needed it as he fixed his gaze on the Satedean. "You don't have to trust him _completely_; all you have to do is accept that he's here and we don't have time to argue about it. Now, can you both just sit back down so that I can do what I came here to do and get you both _out _of here?"

Not giving them time to argue, John turned his attention back to the map showing the Hive's internal layout, quickly turning the engines up to full power and charging along the corridor, only briefly noting that McKay and Ronon were now in their seats- Ronon was still holding on to his blaster, but at least he wasn't aiming it anywhere he shouldn't right now- as he continued to hurtle along the corridors towards the chosen target.

"What are you-?" McKay tried to ask.

"Regrettably, there aren't any windows in these things, and I don't fancy trying to break out of this ship through the dart bay again, so we're just going to have to make a hole in the ship the old-fashioned way," John said, his eyes narrowing as he continued towards his chosen destination, a small area a short distance away from the ventral generators where his earlier attack had weakened the Hive's hull. "Hang on tight..."

His passengers barely had time to register his words before they'd crashed through the brittle hull in front of them, John rapidly shifting the jumper's power from the shield to the cloak before any darts could get a clear shot at them. After spending a few moments hurtling onwards through space, John drew to a halt, turning the ship around to study the damaged Hive with a grim smile as the darts flew around the ship, clearly confused about what had just happened now that the source of the damage had vanished so abruptly.

"OK, you _do _know you're certifiably insane, right?" McKay said, his tone hurried as he looked shakily at the Phantom. "I mean, driving this thing _through _a Hive ship? What were you _thinking_?"

"That I didn't want to waste time or take the risk that someone would find you or the ju- the gateship before I could get you out if I just tried landing in the dart bay and searching for you on foot," John replied, turning back to look coldly at McKay, focusing the intense stare that he'd mastered from years of confrontations with hungry Wraith on the scientist. "Besides, given that it paid off, I hardly think you're in a position to criticise me for taking a risk."

"So what now?" Ronon asked, his eyes flicking briefly in Michael's direction in a manner that John didn't like (He might not feel _entirely _comfortable with that guy, but that didn't mean he wanted the guy dead right now).

"Well, I suppose we-" John began, before the sight of a hyperdrive window opening up behind the Hive ships caught his attention, the four men momentarily tensing in preparation for another Hive to appear before _Daedalus _and _Orion _emerged from the white hole in space.

He'd known that Earth's Asgard-based hyperdrives were more efficient than the Wraith's- smaller ships took less power to get into hyperspace in the first place, so they were able to push greater speed into the actual journey-, and the Ancients had naturally been the best at pretty much everything they put their minds to, but to see them arriving this quickly...

_Damn_, Earth was good.

As he watched, _Daedalus _unleashed a barrage of missiles at one of the hives, while the _Orion_- the gloriously functional _Orion_, back to the wonder she had been when she had first been activated, all the repair work he and the Taranians and Atlantis had put into getting her ready paying off at long last- sent a wave of drone weapons at the second, the drones neatly evading all the darts around the hive-ship to strike it directly, shattering it to pieces in a matter of moments.

The second hive fared better, its darts intercepting most of the missiles fired by _Daedalus _so that they exploded away from the ship, but the hull damage it had just sustained from John's impromptu escape was obviously made more serious by the resulting explosion when one of the nuclear missiles made it through the 'dart defences' (As John liked to think of the Wraith habit of using darts to intercept weapons fire in the place of shields). As the four men watched from their jumper, the hole that they had just emerged from began to splinter and crack, the damage rapidly spreading around the hive like something was rapidly drying out, before _Orion _launched a smaller wave of drones at the second Hive, its shields having easily withstood the attempted counter-attack long enough to take out its next target.

"Just the darts left, and I don't think anyone needs us for those after I already depleted my weapons," John said, glancing briefly at McKay before he turned his attention back to the ship's control panel, tapping a few controls quickly and smiling as McKay and Ronon vanished in a brief glare of Agard beaming technology.

"What-?" Michael asked.

"Lowered the shields in their area while strengthening them around ours; as far as the crews of those ships are concerned, they detected McKay and Ronon in the area, took the shields down long enough to beam them to safety, and took them on board before finishing the job on the Hives," John aid, before he turned back to the control panel, activating the ship's hyperdrive and setting off back into hyperspace. "Well, that's our part played in this fight; time to go home, huh?"

Despite the fact that he still had a long way to go before he got back to Atlantis, John couldn't help but smile.

They'd just defeated _two _Wraith hive-ships in a matter of minutes, and saved Earth into the bargain; all they had to do now was get back to Atlantis-

Something struck him on the back of the head, and John's last thoughts were to curse himself for letting his guard down before he fell into unconsciousness.

* * *

AN 2: Well, hope that met with everyone's satisfaction- and yes, I _did _take some inspiration from that bit in _Star Trek: Nemesis _if anyone wants to know-; next up, we look at just what Michael's going to do with John now that he has the Phantom and a hyperdrive-capable puddle jumper in his possession (As well as Elizabeth facing the usual IOA 'interrogation', of course)


	27. Lost Boy Found

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Hope you like what I've come up with for this chapter- and what's happening in Atlantis will be explored in the next one, I promise-; things are getting a _bit _more complicated right now, but I feel that this sets the scene for the next chapter or so rather nicely...

Mystery of the Phantom

As he took in his surroundings as he woke up, John groaned at the sight around him; as it had been the last few times he'd woken up, it hadn't changed from the basic laboratory that Michael had established on whatever planet this was after they'd landed here in the gateship, John strapped down to an examination table of some sort and allowed 'out' only after he was stunned and taken to another room to eat and attend to hygiene-related issues.

He'd been here for a couple of weeks already- assuming that Michael's comments about how long he'd been drugged had been accurate; he'd done his best to keep count after regaining consciousness, but some time had definitely gone by before he'd managed to completely wake up that he couldn't account for-, and so far Michael was showing no signs that he was going to give John any clue about what he was trying to accomplish here. John had tried to remain silent so far in the hopes that Michael would answer his questions for the sake of hearing himself talk rather than anything else- most of the Wraith John had encountered were fairly egocentric when dealing with captives, after all-, but he had yet to say anything more than the news that he'd been unconscious for 'a while' after he woke up and otherwise leaving the matter alone.

God... he'd tried to trust Michael, and then the bastard went and knocked him out because he 'couldn't take the chance' that John would take him back to Atlantis; John could have just dropped him off on a decent planet and let him make a life for himself, but Michael hadn't even given him the goddamn _opportunity _to even do _that _much!

Even if the hybrid had turned against him, however, John was grateful that Michael had been able to steer the jumper to this planet- judging by the pain in his wrists, he assumed that Michael had made him keep his hands on the controls so that the ship still sensed that he was physically giving orders even if he wasn't conscious; the jumpers might be primarily controlled mentally, but it wasn't like they'd stop if the pilot was knocked out-; he might be a prisoner here, but at least he wasn't dead in space.

The situation might be grim, but where there was life, there was still hope; he had to focus on that if he was going to get out of this situation at some point.

Plus, of course, he could at least be grateful that Michael hadn't removed his mask; he probably couldn't have done much to the technology inside it even if he'd been able to get past some of the anti-Wraith measures John had installed- including humans as something that the mask would prevent removal by had been considered and discarded when John realised that he didn't know how to design sensors that would ignore all other humans but him; programming Atlantis's sensors not to track him had been challenging even when someone else had done most of the hard work in designing the systems already-, but it made John feel better to know that the other man didn't know what he _really _looked like under the mask.

It was unlikely that Michael would have been able to figure out what was _really _responsible for his appearance underneath the mask- the circumstances that had led to him looking like this were fairly unique-, but that didn't mean John wanted more people to get the wrong impression about him; his early experiences of travelling without the mask had been more than enough of _that _for him...

Right now, he just needed to focus on the immediate priorities facing him, which included determining his current location and the reason for their presence there. Judging by the general atmosphere of the place, they were apparently in some old Wraith research facility on a planet on the outskirts of the Pegasus Galaxy- John hadn't been able to establish whether or not it had a Stargate, but he was guessing that it was gateless or at least didn't have a Stargate in a convenient location, given that those facilities were generally established on worlds where the Stargate wasn't immediately accessible to ensure that nobody stumbled across their work by accident; the mess that resulted in Teyla and other Athosians possessing their 'gift' had taught the Wraith to avoid repeating those circumstances-, and, from what John had seen, Michael was working to access the laboratory's computers for some reason or another.

How Michael had known about this stuff was something John didn't know- had he regained some of his Wraith memories about who he'd been, or had he stumbled across something in the hive's databanks before they'd turned against him?-, but it also wasn't something he really needed to concern himself with right now. Given Michael's apparent pariah status among other Wraith after his transformation, coupled with his recent role in helping John, McKay and Ronon escape- even if he had turned on them afterwards-, he probably wouldn't have to worry about dealing with more Wraith in this situation any time soon, which meant that he still had a chance to get out if he was careful...

"Still contemplating escape?" Michael asked, his voice drawing John away from his thoughts as he looked up at the man on the other side of the door to his room (He couldn't call it a cell as the door wasn't locked; he just couldn't walk over to it), his own gun hanging from Michael's belt as though the hybrid was daring him to take it. "Haven't you given up by now?"

"I think we both know that I didn't become the thing the Wraith have nightmares about by giving up that easily," John countered, clenching his fists as he stared resolutely at Michael, resisting the temptation to try his only viable plan so far; if he tipped his hand before he knew how he was going to go any further, he'd be in even more trouble than he already was and would lose his own real advantage. "What do you even _want _with me, anyway? If you seriously think that I would _ever _help you of my own free will-"

"Let's just say that you could be... useful to me down the line," Michael said, chuckling slightly as he walked around John, flexing his fingers as though anticipating what it would be like to take John's body apart. "After all, you _are _a very unique specimen-"

"If you think I'll _ever _help you in _anything_-" John spat scornfully at the hybrid (How he'd ever hoped that this guy could have been a kindred soul he didn't know; the bastard was just out to destroy anything that _might _threaten his safety).

"You will give me something _eventually_," Michael said, shaking his head in satisfaction. "Even if you don't choose to aid me willingly... there are always ways to get what I'm after."

"And what would those be?" John asked scathingly. "We both know that I've endured the worst that you Wraith have to throw at me to get me to comply using your normal methods, and I always ended up turning them against you; what are you going to do that they didn't, stick some kind of implant on me or something?"

"Tempting, but imprecise and unlikely to succeed anyway," the hybrid replied dismissively. "No, what I plan for you is far more long-term than that... to say nothing of less _direct_-"

The sound of something yelling in pain outside the door of John's cell forced him to abandon any thoughts he had of waiting any longer to break out.

He might not know much about his current location, but he did know when something was in pain, and if Michael was carrying out further experiments in this lab, that just made it all the more important for him to stop this bastard before he could do anything else; John could take whatever this guy had to deliver if he had to, but another victim in this place was another potential ally for John as far as he was concerned.

As though he was being held down by nothing more than string, John suddenly broke the straps that had been keeping him apparently trapped, his feet landing on the ground as Michael drew the weapon he'd taken from John and fired it at him, only to be shocked when the gun's red energy shimmered over the distinctive green pattern of an Ancient shield device that John had kept concealed in his cloak, just close enough to his skin to be activated without Michael realising that it was there. Before Michael could fully process what was happening, John had punched the hybrid in the face, the additional power of the force field boosting John's already above-average strength to send Michael slumping to the ground, completely unconscious.

"Take all the time you want to rest, you bastard," John said, glaring scornfully at his enemy as he took his gun back before he turned around and ran out of the cell, hurrying down a corridor in the direction of the scream that he'd heard earlier. Finally reaching a likely-looking door- it looked fairly thick, but it was also slightly open; Michael had probably been here earlier and forgotten to properly lock it-, John opened the door, and nearly felt like throwing up at the sight that greeted him on the other end.

The entire room was filled with a massive web of purple vein-like things that put John in mind of a Wraith hive-ship, of varying thickness and length, all of them reaching out to the ground, walls, or ceiling, and all of them originating from the same source; a young man, lying bound on an operating table in the middle of the room similar to the one that John had been imprisoned on, his face immediately familiar to John despite the burns and further disfigurement around one eye.

"Lieutenant Ford?" John said, his eyes widening in shock as he took in the sight of Atlantis's most prominent MIA member; he wasn't sure if the man was even conscious in this sort of state, but addressing him directly seemed like the most effective way to establish that.

"Ugh..." Ford muttered, blinking his eyes open- the formerly-black eye now back to normal, even if the skin around it was still strange; judging by his appearance, John guessed that something had happened that made Ford briefly pass out from pain as he let out the previously-heard scream, but things appeared to be more stable now- and taking in the room around him in momentary confusion until his gaze focused on the Phantom. "_You_-!"

"Easy!" John said, holding up his hands in a defensive gesture; Michael would probably be out for a while, but anything that might stir him into consciousness was definitely _not _to be encouraged. "I know you're probably mad, but don't freak out on me before you've had a chance to think; I'm here to help you-!"

"You want to help?" Ford said, glaring over at the man he knew only as the Phantom as he tried to move his arm; John wasn't sure if Ford had fully registered where the things filling the room came from or if he was just focusing on his own anger. "Make those goddamn voices _stop_!"

"Voices?" John repeated in confusion, taking a brief pause to listen again in case he'd missed something earlier before he refocused his attention back on Ford. "There aren't any..."

As his gaze refocused on the tendrils extending outwards from Ford's body, John wished that he could think that his current theory was wrong; it might be based on minimal evidence, but those things looked _far _too much like the interior of a hive-ship for John to feel comfortable deluding himself that he was dealing with anything other than the worst-case-scenario (Besides, if he assumed the worst, anything else he encountered or learned to the contrary would be a pleasant surprise, even if he wasn't optimistic about the odds of that actually happening given some of his past experiences).

"Oh no..." he said, glancing around the room urgently for a few seconds before his eyes fell on an old Wraith computer; it was antiquated by any standard- it looked like it was from an era before they'd even fully mastered using organic computer systems and were using scavenged Ancient technology-, but that didn't matter right now; as John hurried over to the computer and began to scan through its files, all that mattered was what it had to tell him rather than how it was stored.

"What are you...?" Ford asked, turning his head to look at John as much as his position would allow him to do so.

"Looking for information on what Michael's doing to you," John replied grimly, his fingers practically flying over the controls as he searched through the database (He noticed some brief references to Michael finding Ford a day or so ago, which at least suggested that this planet had a Stargate, but then he noted Michael's reference to 'disabling' the DHD and scratched that possibility as a way of getting off this world). "If I'm right, than..."

He trailed off, realising as he spoke that he wasn't entirely sure what he could do about the situation if he _was _right, before shrugging and turning his attention back to the computer. "Well, on the bright side, the Wraith and Ancient written languages aren't that different from each other- and don't ask me how that's possible because I just don't know for certain any more than you do-; all I need to do is make the necessary adjustments to accommodate some of the slight linguistic differences- you don't fight the Wraith as long as I have without picking up some useful details about how they communicate-, and we _should _be able to..."

His eyes widened as he registered the information now displayed on the screen in front of him, and John couldn't stop himself from letting out one of the few swear-words he allowed himself to say these days. "Oh, _shit_."

"Bad?" Ford asked, looking at the man he knew as the Phantom with increased apprehension, his usual hostility against the man in the mask forgotten in the face of the fear and regret that was visible despite the limited amount of his face that was exposed to outside view.

"You've been infected with a Wraith pathogen," he said, looking grimly back at the other man. "I'm not clear on the _how _of it, but based on the references here to this thing generating an organo-metallic polymer... I'm guessing that this is going to become a hive-ship."

"A _what_?" Ford said, staring at him incredulously before he indicated some of the tendrils coming out of him with an awkward wave of his hand. "You're saying that this... _stuff_... is going to become a _hive-ship_?"

"It's a bit worse than that, actually," John said, looking regretfully at Ford, wishing that he had a better idea how to phrase this; he might be brilliant in a fight, but he _sucked _in social situations. "If the infection runs its course... you yourself will _be_ the Hive-Ship."

"_What_?" Ford said, clearly incredulous at the idea.

"Well, they are essentially living things; it's not like they all started out that size," John said, smiling slightly at Ford even if he knew that it was a mistake as soon as his lips started to twitch; there was nothing he could do to lighten the mood in this situation, so he shouldn't really even bother to try. "How long it will take I can't say- Hives are always restricted by their power requirements, and in your case you're starting out with access to limited external power even if you're physiologically more capable of weathering the stress of the transformation than others might be; a side-effect of that enzyme, I suspect-, but the fact remains that you are _going _to become a Hive-"

"How the _Hell _did this fucking _happen_?" Ford yelled, shaking off his initial shock to focus on the immediate facts. "I'm not a fucking _Wraith_-!"

"No, but it wouldn't exactly be impossible to infect you with the relevant pathogen; once it gets into your system, it'll only take so much time until it finally consumes your physiology and coverts it for its purposes," John said, looking grimly at the lieutenant. "Once it reaches a certain point, it'll consume your brain and your consciousness will be replaced with that of the Hive; it's having trouble reaching that stage given the lack of energy sources available for it to draw on right now, but your enhanced strength is giving it a lot more to tap into than it would normally have in this situation, and the fact that you can hear those voices suggests that it's starting to manifest some degree of intelligence-"

"Shut up about what this thing is doing to me; just _stop it_!" Ford yelled in exasperation, wincing as he tried to wave one hand, the strain of even that much physical activity apparently too much for him in his current condition. "You're the goddamn _Phantom_; you've got to be able to do _something_-!"

"There's nothing I can _do_, Lieutenant Ford," John said, glaring at the other man. "If we had enough time and Doctor Beckett or someone like that was here, maybe we could pull it off, but my knowledge of even human biology is limited, never mind Wraith biology; I can keep myself healthy and kill Wraith fairly quickly, but treating something like this is _way _beyond my abilities."

"You have to do _something_!" Ford yelled urgently at him, panic becoming obvious as his fragile control of himself began to fall apart. "I _won't _become a-!"

"If I had time to put the cure together and someone had established some kind of foundation that I could use to start things off, _maybe _I could do something, but I can't create an antidote to something like this from _scratch_!" John yelled- he might be exaggerating his skills, but he liked to think of himself as fairly adaptable and he _knew _that he was intelligent, so he might have been able to do _something_ if the aforementioned rules applied and someone else had given him something to work with-, before he paused and took a couple of deep breaths, trying to calm himself before he looked back at Ford. "If I could save you, I would- whatever you think of me, I've never wanted _anyone_ in Atlantis to die; all I've ever wanted to do is protect that city-, but I can't cure this; I don't even know what could hurt it without hurting you!"

After a moment of silence as the two stared at each other, a grim expression on Ford's face and a pleading one on John's, Ford sighed in resignation.

"Fine," he said, his gaze flicking down to John's waist. "Use that."

"Wh-?" John began, before he followed Ford's gaze and realised what the other man was looking at; the gun he'd just taken back from Michael. "Are you-?"

"_NO_!" Ford yelled, staring with near-frantic intensity at him. "I _won't _become a hive; if you can't help me, _kill me_!"

For a moment, John could only stare silently at back at Ford, his knowledge that Ford's suggestion was all that he could do for him warring with John's simple promise to himself not to kill human beings unless he knew that they unquestionably deserved to die.

He'd avoided killing even Kolya when nobody could have blamed him for shooting the guy in the head after ensuring that Elizabeth was out of harm's way; he would _not _kill Ford...

"Look," John said, glaring at Ford, "I'm not going to kill you, and there's still time to cure you of this; right now, our immediate priority _has _to be to get out of here and find some way of helping you."

"And how would you recommend we do _that_?" Ford asked.

"Actually, my plan ties into what's being done to you right now," John replied with a slight smile. "Theoretically, since you're becoming a hive-ship, some part of you is already growing the components that they all possess; if we focus, you _might _be able to access some of them in their larval stage and accelerate their growth-"

"You want me to try and _help _this thing-?" Ford began.

"-focusing on the long-range communication systems that might allow us to establish contact with Atlantis," John finished, smiling encouragingly at the lieutenant; he might know how grim the situation was, but since he doubted that the lab had access to a communication system in itself, he'd have to work with what he had. "The enzyme's allowing you to better cope with the transformation; maybe it'll give you some degree of control if you focus on what _you _want the pathogen to generate."

"We're in a completely different _solar system_; we'll be lucky if we can get _any _kind of signal through-!" Ford countered.

"We can at least send off a Morse code message or something; once they know something's here, that's half the problem dealt with," John said, looking resolutely at Ford. "Just send concentrated pulses of information to Atlantis, focusing on the right length for each, and we _should _be able to pull this off..."

John just hoped that he sounded more confident than he felt; even if Ford could find the communication systems in whatever his body was trying to become and use them in the manner described, there was no way to guarantee whether or not Atlantis was in a position to respond to their request in time even if they understood it...

Still, he had to try.

Even if he was reasonably sure that he could find the puddle jumper that Michael had used to get here in the first place somewhere on the base with relatively limited effort- Michael wouldn't want to destroy the only means of transportation available to him, even if it he probably couldn't use it-, he wasn't going to abandon Ford here unless he had absolutely no choice.

It was time to see whether those meditation lessons he'd received when he was stuck in that temporal field thing were worth anything when he was trying to _teach_ those skills to others; if he could just help Ford focus his mind on his goal, the chances of them _both _getting out of here might get better...


	28. The Low Point

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: I had to make a short jump forward for this chapter, but it wasn't that much further than the one we experienced in the episode itself (Even with the Asgard helping Elizabeth and Woolsey return to Atlantis, they can't have been that much faster than the ZPM-enhanced _Daedalus_, and it still would have taken a few days for the _Daedalus_ crew to get sufficient control of that Wraith ship to take it back to the city)

AN 2: Sorry about the delay in this chapter; real life and writer's block, you know

Mystery of the Phantom

As she sat in her office in Atlantis, Elizabeth wished that she could bring herself to feel more relaxed now that she was back in her home (Even now, a part of her almost couldn't believe how comfortable she felt in this alien city after less than two years in Pegasus; she was in a city that defied almost everything she had come to expect, at threat from an army of life-sucking aliens. patrolled by a man in a mask whose real name may still be a mystery to her, and she still felt _safe _here?); the mere thought of Richard Woolsey's continued presence in the city made even the possibility of relaxation near-impossible.

Getting back to Atlantis hadn't actually been that difficult- they'd called in some favours from the Asgard to provide a ship that could take her and Woolsey back to the city in a few days-, and at least _Orion_ and _Daedalus _had come through the recent battles relatively intact, but she had more than one problem facing her right now. Not only was there the obvious issue of Woolsey carrying out an evaluation for the IOA, but there was also the more personal problem of John's continued absence from the city; nobody had seen any sign of him since he had rescued Ronon and McKay from the Hive, even with the entire city on alert in case any other Hives or any kind of ship appeared anywhere within range of Atlantis's sensors.

Right now, she just wished that she could get past the varying degrees of fear facing her and get back to dealing with a crisis that she could actually deal with herself; maybe it was John's attitude rubbing off on her, but this current mess with the evaluation and the possibility of her losing her command of the city was frustrating her precisely because she had absolutely no way of resolving it quickly and efficiently other than just letting the situation play out however it would.

She supposed the thing that made it worse, of course, was the fact that two of the most senior members of the expedition- even if one of them was only peripherally affiliated with Atlantis on a semi-regular basis- couldn't be guaranteed to speak up in her favour. Caldwell had a certain respect for her abilities, but she wasn't entirely certain how much of that respect was due to her decision to keep Sumner on as the expedition's military commander rather than respect for her as a person, and Sumner himself, while loyal to the chain of command, still expressed the occasional doubt about her occasional dependence on the Phantom to help them out when the situation they were facing became particularly desperate (She was just grateful that he hadn't expressed any objection to their recent alliance with the Wraith; at least he recognised that they'd all been at fault rather than trying to absolve himself of blame by pinning it all on her).

She had tried to hold the city together in the face of the ever-increasing threat of the Wraith, and now, here she was, facing the possible end of her career in Atlantis, and the people whose opinion would really make an impact on the IOA probably wouldn't even care enough to support her.

She supposed that she should just be grateful that they'd managed to destroy both Hives without resorting to more desperate measures like, for example, trying to defeat the Wraith with the retrovirus; even if it had actually worked, it would have left them with far more problems as they tried to figure out a way to make the retrovirus's effects permanent before the human Wraith regressed back to their original natures like Michael had, to say nothing of how the IOA would have reacted to them having to deal with that kind of issue...

In the end, however, what was almost the most disturbing thing about her current situation was that she was regarding a man in a mask as a regular source of stability in this increasingly chaotic world.

As much as she might have laughed at the idea in the past- if she was honest with herself, in the past she would have found it disturbing to see any other person display this level of faith in someone under these circumstances-, it didn't change the facts; out of everyone she worked with in Atlantis, the man she relied on the most had never shown her his real face and she didn't even definitely know his real name.

Nevertheless, even if the IOA or Stargate Command weren't entirely comfortable with his presence, Elizabeth would _always _believe in John's loyalty to Atlantis; he had done and risked too much for their sakes for _her_ to ever doubt him, no matter how much her superiors back on Earth might oppose his presence.

She just wished that she knew where he was _now_...

"Doctor Weir?" Chuck suddenly said, breaking into her train of thought as he stood anxiously at her door.

"What's wrong?" she asked, looking uncertainly at him; everything seemed fairly calm outside, so it probably wasn't an approaching Wraith vessel, but in an unknown location like Pegasus the list of things that could cause concern without being obviously dangerous were relatively high.

"We're receiving... well, we're receiving a rather strange signal on the long-range sensors," Chuck said, looking suddenly awkward as he looked at her. "It's basically just some kind of intense energy pulses from some distant part of the galaxy- we'd probably assume it's some kind of natural phenomenon if they weren't so regular and coming from subspace-, but... well, they seem to be an SOS."

"An SOS?" Elizabeth repeated, sitting up sharply before she got up from her desk and walked into the main control room, where McKay, Sumner and Caldwell were already staring at the main display screen, which currently showed a basic galactic map with what she could only describe as an intermittent beam coming from one corner of the map.

"What is it?" she asked, looking at her chief scientist.

"In basic terms, something's churning up subspace to send us a seemingly random signal across a great distance," McKay explained. "It's basically similar to old radio transmissions back on Earth; before we had the ability to send anything more sophisticated like actual speech, we just relied on basic signals like this one."

"That's actually one of the things that has us concerned," Sumner said as he turned to look at her, even if his tone made it clear that 'us' referred primarily to himself and Caldwell. "Considering recently events, we have to consider the possibility that the Wraith picked up details of how to use this code from the information they acquired during our brief alliance-"

"Oh, of course; they looked up a code that is so old as to be virtually obsolete, and then choose the most basic pattern in the book," McKay said, shaking his head in frustration. "I know I'm not a military genius, but I studied the information about what they stole, and they did _not _take anything to do with our ability to communicate; even if they did, anyone who knew Morse code without knowing the background information would try and use something more sophisticated because they'd think we'd be more likely to fall for it. The only people who'd send such a basic message would be people who came from here without knowing anything more than the basics, and they wouldn't send something like that unless they _really _had no other way to get in touch with us."

Elizabeth was just grateful that McKay didn't say anything about the possible identity of the sender; regardless of how much help he'd offered them in the past, the possibility that they were being contacted by the Phantom might make the colonel a _bit _more reluctant to take action...

"All right," she said, looking over at her senior staff. "What are our options?"

"Well, _Orion_'s more advanced, but _Daedalus_ is probably better for getting in and out undetected; I've been working on a way to modulate the shields to absorb Wraith scans so that it looks like we're not there, but the catch is that it'll leave us vulnerable to attack if we're spotted and can't switch in time-" McKay began.

"Then we'll just have to ensure we aren't spotted," Elizabeth said, looking firmly at McKay before she looked over at Sumner and Caldwell. "We'd better get moving; the sooner we can determine where that signal came from, the better."

"Understood," Sumner said, standing up as he and Caldwell headed for the door to the conference room.

"The rest of you..." Elizabeth began, turning to address the other three members of Sumner's team before she realised the pointlessness of it; as a professional soldier, Sumner had made it clear more than once that he wouldn't take his team with him in a situation where they weren't needed, and with the _Daedalus _crew available this was definitely one of those cases.

"...just do what you can here," she finished, shrugging slightly uncomfortably at them out of a lack of anything else to say or do.

"And... send a series of pulses back," she added, looking over at Chuck with a slight smile even as the rest of her staff left the room, grateful to remember that there was something she could do in this whole mess. "If there's someone sending that, we should let them know we're on our way."

They might not be able to receive or understand it- if someone was sending something like that, it seemed likely that their communication options were limited-, but she had to do _something _to let the person at the other end know that they weren't alone, particularly if it was who she thought it was...

* * *

"Ugh..." Ford muttered, shaking his head in frustration, his movement limited by the tendrils that continued to grow around his body.

"Well?" John asked, looking hopefully at the face of the still-mutating lieutenant, trying not to pay too much attention to the mass of tendrils that were still emerging from his body; if he didn't think too much about it, it was easier for him to deny the scale of what he was facing and focus more on what he could control.

"I'm..." Ford said, wincing slightly as he closed his eyes, a focused concentration clearly visible on his face, before he opened them and looked at the other man. "It's confusing, but I'm getting something back... three long pulses... a long and a short one... three long ones..."

"'On our way'," John said, smiling slightly as he looked at Ford. "It's the signal for 'On our way'."

"There's more-" Ford began.

"What you've given me is enough to know that's what the rest of the message would be," John said, smiling reassuringly at the younger man. "Just hold it together and stay calm, Ford; I'll just go and make sure that Michael's still locked down, and then we should be ready to move on when everyone gets here."

The hyperdrive-capable gateship might still need to be found- he doubted Michael had taken it too far from here, but it wasn't like he'd had the time to look and see what else Michael had done to it even if he couldn't fly the thing on his own when Ford was the first priority-, but if he had his way, they were _all _going to get out of here...

It was only when he walked out of the room where he'd been staying with Ford and saw Michael standing in the corridor with a drawn weapon that looked like a sharper version of the Wraith stun pistols that he realised that he'd spent too long with Ford; why the _hell _hadn't he tried to lock the damn door?

"Oh," he said, deciding to go with feigned nonchalance and hope for the best; given the Wraith's arrogance, acting like you _weren't _afraid of them was often the best way to get them to make mistakes. "You woke up."

"I did," Michael replied, glaring resolutely at John as he flexed his fingers in anticipation before he charged towards his opponent. John barely managed to shift into a combat stance that allowed him to throw Michael off to the side before the hybrid could grab him by the throat, leaving the hybrid pinned to the wall as the masked man stared at him.

"_Damnit_, Michael; would it _kill _you to stop acting like it's kill or be killed here?" John yelled, glaring in frustration at the hybrid. "Is it such a crime for people to want you to become something that _doesn't _feed on people?"

"When it involves destroying who I am _now_, yes," Michael practically spat at the Phantom, reaching up to grab John by the upper arms, gradually pulling the arms holding him down away from him. "You cannot simply cure what I am like a disease-"

"Your body can't cope on its own; I call _that_ a disease-!" John protested, still straining against his opponent's grip.

"It is no more a disease than your need to eat to survive-" Michael began, glaring firmly at John as they continued to try and force the other to release their grip.

"Which doesn't involve taking what other sentient beings need to survive themselves; if you can't survive without others dying for you, I'd call that a problem!" John countered, before he rolled his eyes in frustration at the increasingly repetitive nature of the current debate and rammed his knee upwards between Michael's legs; as much as the moral debates would be interesting mental exercise in other circumstances, right now his priority was Ford. As Michael's grip instinctively lessened as he moved to clutch in pain at the part of himself that had just been hit, John shoved him away before lashing out with a spinning kick- an extravagant move, but he liked the effect it created when he did that with the cape- that struck Michael in the face, sending him flying backwards into the nearest wall.

"Can't we just _talk _about this?" John asked, glaring in frustration at Michael. "We are _trying _to help you here-!"

"And who is to say that this is not helping Lieutenant Ford, if we use your defence?" Michael asked, taking a small object from his belt and holding it up in front of himself. Before John could react, Michael pressed a control on the small device, and suddenly John heard a loud scream of agony from down the corridor where he had left Ford earlier, far more intense than the scream he'd heard earlier.

"NO!" John roared, firing a quick 'force-blast' at Michael- he wasn't sure what the technical term was, but it basically dialled down the gun's energy output so that it only generated a brief burst of energy that left you feeling like you'd been hit with a large beanbag; solid enough to knock you down, but not to the point that you'd break something in the process-, that sent Michael flying backwards, only for John's smile to turn into a frustrated glare when he realised that Michael had just fallen through a door. Even as John started to charge towards the door, Michael somehow managed to raise his head enough to glare at John and kick the door shut, a clicking sound emerging from the solid door that represented the universally-recognised sound of a lock clicking into place.

Cursing as he slammed his palm against the now-sealed door in front of him, John paused to shoot the lock- if he couldn't get Michael back to Atlantis for treatment willingly, and the guy was _this _willing to delay him getting picked up, the bastard could just stay here and get blown to smithereens- before hurrying back to check on Ford, praying that his worst fears for the younger man weren't about to be realised...

As he arrived back in the room where he'd originally left the lieutenant, however, John quickly realised that he was indeed dealing with the worst-case scenario. When he'd activated whatever that device had activated, Michael had either triggered some kind of implant or just activated something connected to the tendrils that John had missed in his earlier examination of Ford; judging by the faint steam coming off his body, Ford had just received a not-inconsiderable electric shock, with the result that his pathogen-infected body had automatically tried to respond to the pain in the manner that it was currently best suited for, thus causing the mutation he was currently undergoing to accelerate significantly in order to keep Ford's body in working order.

Whatever it was that Michael had activated, the result of it was that the lieutenant's mutation was now progressing at a far more rapid rate than it had been before he'd taken action, which meant that John's chances of getting the lieutenant back to Atlantis before the mutation had progressed to a point beyond any cure that they might be able to give him would reverse the process...

"It's... not... good... huh?" Ford said, his every word an obvious strain, as though he was not only having trouble speaking but was also having trouble remembering what word to use to convey what he wanted to say.

"No," John said, shaking his head grimly as he looked over Ford; tendrils actually seemed to be emerging from Ford's fingers as though they were extensions of his body now, rather than just something that was growing out of him. "Whatever Michael did to you just now, the pathogen was able to use your weakness to gain a better grip on your physiology- probably 'decided' to evolve into something that could better cope with what you were going through-; as far as I can tell, you're..."

He fell silent, trying to figure out the best way of saying this, but Ford beat him to it.

"In other words, I'm screwed, huh?" he said, looking grimly at John.

"Yeah," John said swallowing awkwardly as he looked at Ford, his eyes earnest behind his mask. "Trust me, if there was anything that I could do to help you, I'd do it, but the shock you received has accelerated the spread of the pathogen; even if you're mentally more in control of yourself than I'd expect, you're going to succumb to this thing before anyone can do anything..."

"Fine," Ford said, looking grimly at the other man. "Shoot me."

"What?" John said, his eyes widening in horror. "I can't-"

"_Shoot me_!" Ford said, glaring at the masked man. "If you can't stop this, kill me while I'm still able to think about it; I'm not going to become a fucking _hive-ship_!"

"I can't even guarantee you'll be able to _die _in this shape-" John began, trying to find a way around what he was being asked to do (The fact that the pathogen might heal anything he did certainly helped him in that regard; he couldn't predict what the consequences of a direct attack would be when Ford was in this kind of shape).

"Take my fucking head off, then; just don't let me die like that!" Ford said, raising an arm a few inches before giving up when the tendrils prevented him from moving it any further, terror obvious on his face. "I don't care what it takes; I _can't _lose myself to _this_!"

For a few moments, John could only stare at Ford in silence, his mind racing as he tried to figure out what he could do next even as he knew that nothing he had available would make any difference to the situation at hand, until he finally raised his gun with one hand and drew his sword with the other.

"Shot to the head should put you down, and then I cut it off before the pathogen can start to heal anything," he said; no matter how grisly it was, Ford deserved to hear what was about to happen to him. "Lieutenant Ford, believe me, if there was _any _way I could cure you-"

"I know..." Ford said, smiling slightly at him. "You're... the Phantom... right? You save people..."

"And I will save Atlantis," John said, nodding solemnly at the other man. "Until I don't have the life in me to do so, I _will _protect that city from whatever will threaten it in the future."

"Good..." Ford said, smiling briefly at the other man before he closed his eyes and laid his head back against the table.

Not giving himself time to hesitate, John fired the gun with one hand before he thrust his sword forward, turning away from the sight and only allowing himself to briefly register the sickening slight thump as something hit the floor.

With that bloody business done, he left the room, sealed the door behind him, and hurried down the corridor, pausing only just long enough to check each door he encountered until he found the one he was looking for; a large, open room with a ceiling that had clear signs of moving parts within it, along with the welcome sight of the hyperspace jumper in the middle of the room along with a couple of Wraith darts. John briefly noted that the darts appeared to have started to decay slightly- most likely they had been left here in this base when the Wraith had originally abandoned it for whatever reason they'd left it-, but pushed that thought aside as he entered the jumper, his attention focused on making sure that everything was where it should be. From what he could determine, a couple of crystals relating to the ship's databanks had been removed, but they didn't control anything vital and they would certainly get destroyed when the Atlantis expedition reached the base.

Settling down into the chair, John started the ship's engines, turned the force field up to its strongest setting, and tore out of the base, shattering the ceiling as he left; he wasn't going to stay in that place of death for any longer than he had to. After taking a moment to ensure that the base's power supply was still active- it wasn't that much power, but on a planet with no other forms of technology it wouldn't exactly be hard to find it-, John turned around and set a course back towards Atlantis, determined to leave the whole bloody mess behind him.

* * *

A few hours later, as Elizabeth stood on her balcony, she couldn't believe that she was actually still here.

The exact origin of the SOS was still a silent question-mark- she, at least, was fairly certain that she knew what had sent the original message, even if she'd been fully aware that she couldn't provide anything to support that theory-, but they'd at least been able to destroy the facility after the _Orion _had arrived there and sensors had confirmed that the only living things in the base were a Wraith and the anomalous life-readings that they'd learned signified the presence of Wraith ships; according to all reports, the attack on the base had been so thorough that nothing was left standing.

Add in the fact that Woolsey's report had favoured her remaining in command- even if he'd slightly bent the rules by claiming that she'd given orders to fire on the base immediately after the _Orion _dropped out of hyperspace when she'd actually requested that Sumner wait to confirm that there were no humans alive in the base before taking action-, and things were generally going rather well for them after their recent run of bad luck. The Wraith were down two hive-ships, Michael was gone, and Atlantis's location remained secret; all in all, on a galactic scale, things in Atlantis had never been better.

_Almost never_... Elizabeth thought to herself, allowing herself a momentary sigh as she stared out at the sea before her.

Even after everything else they'd accomplished, she didn't know what had happened to the Phantom... to John. Sumner and the others might not be that concerned about it- Teyla didn't seem to think that the Phantom was even _capable _of dying sometimes-, but the fact that she still hadn't heard from him since the last message he'd sent before leaving Atlantis was not encouraging...

"Hi, Elizabeth," the voice she'd been waiting to hear said from behind her.

"_John_!" Elizabeth said, not even bothering to suppress her grin as she turned to look at him, only for her smile to falter at the dejected expression on his face. "What... what's wrong?"

"Ford was there," John said, his expression grim under the mask as he looked at her. "Michael had captured him."

"_Ford_?" Elizabeth said, her eyes widening incredulously. "But-"

"I don't know how, but he was there; Michael had infected him with some kind of freaky Wraith pathogen and was working on mutating his body into something that... well, it wasn't human," John said, sighing as he walked over to lean against the railing, a defensive aspect to his posture that Elizabeth didn't need her long experience with body language to read. "I did what I could... but then Michael activated something that forced the infection to spread..."

He swallowed slightly, his jaw tightening as though trying to prepare himself for the worst, and then he looked back at her, clearly wanting her to understand what he was about to say. "I couldn't save him."

Elizabeth could tell that there was more John wanted to say about that particular topic, but she didn't give him the chance to say it; on impulse, without even thinking about it, she walked up to him and wrapped her arms around him, giving him as reassuring a hug as she could manage.

"You did everything you could, John," she said, smiling slightly as she felt him wrap his arms around her in response to her efforts. "If you could have saved Ford, I _know _you would have; don't beat yourself up because you failed."

It wasn't exactly the best therapy she could provide for him given his obvious grief at his failure to save the former lieutenant, but, in his current state, it was the best that she could do for him.

She knew so little about this man who'd dedicated his life to protecting the city that they'd come to call home long before any of them knew that it had any kind of existence beyond the ancient legends, but what she knew of him left her reassured that he could be trusted to do everything in his power to help them; that was all that anyone could rely on in a world so far outside anything they knew.

Even if she couldn't safely convince anyone else to have her level of faith in him, _she _could believe in him...

* * *

AN 3: Hopefully, I'll have the next chapter up sooner; the current plan is to include John's thoughts on seeing SG-1 during 'Pegasus Project', and then the next chapter will explore his thoughts on a very particular git...


	29. The Fallen Ascended One

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: A quick look at John's perspective on the events of 'Pegasus Project', set towards the end of the episode; hope you like it

Mystery of the Phantom

As he crouched in position a short distance above what he had come to think of as 'his and Elizabeth's balcony'- it was probably a bit excessive to think of it like that, but they _were _the only two people who used it regularly in Atlantis's normal routine-, John could only watch as Doctor Daniel Jackson and Vala Mal Doran looked out at the ocean before them, the two members of SG-1 reflecting on what had taken place in Atlantis during the day.

"She did what she believed was right, Daniel," Vala said, looking at the formerly-Ascended archaeologist with an attempt at an encouraging smile. "How badly can she be punished for that?

"I don't know," Daniel said, staring contemplatively out at the sea (Evidently, the memory of what he'd experienced during his time among the Ancients still had a significant impact on him, even if he couldn't remember most of the first time and had only partly Ascended on the more recent occasion;

"Maybe she'll just get a slap on the wrist," Vala suggested uncertainly. "Or be forced to write 'I will not interfere in the affairs of humans again' ten thousand times."

"Yeah, I doubt that," Daniel said, his gaze still on the ocean before them.

Looking at him as he stared out at the darkened horizon, Vala sighed and took up position alongside him, staring out at the sea.

"She said you had your answer," the ex-thief pointed out, looking hopefully at him. "We found out the two addresses we came here for. Can you at least… smile about that?"

"I suppose," Daniel said, still staring out in dejection. "But we did find out something else, too."

"What?" Vala asked, raising the question that John was wondering about himself.

"They're not going to help us," Daniel said simply. "We're in this alone."

This was one area where John felt his inadequacy when compared to the original Ancients more keenly than ever; his near-complete ignorance of Ascension and the rules defining it.

He'd learned some of the broader details about the mental state required during his time in the valley, of course, but knowing the basics of what you had to do to reach that point that point didn't mean you understood anything about the rules and restrictions that the Ancients had imposed on themselves after they'd achieved it; Chaya was the only actual Ancient he'd met since he came to the city, and he just hadn't felt right asking her for more information than what she'd told him already after he'd turned down her 'offer'.

He just wished he could feel more optimistic about their chances if the situation had become so serious that Morgan- or Ganos Lal, whatever she preferred to call herself- was willing to risk punishment to give them even the limited information she'd been able to tell them before she'd been banished.

Still, in a way, it had been rather interesting to learn how Merlin- or Moros, whatever he went by- had managed to construct the Sangraal. The idea that he'd managed to retake human form while retaining most of his knowledge and powers was actually kind of fascinating on its own, but that he'd done so to directly defy the others and protect the lower beings...

After what Elizabeth had told him about Moros when he'd first arrived in the city, the idea that the guy had moved on from rejecting her attempts to return to the future to sacrificing life among the Ascended in order to protect everyone else in existence... it was actually kind of encouraging, in a strange way.

For a moment, he thought about jumping down onto the balcony to have a brief talk with Doctor Jackson- given the other man's experience with the Ancients it might have been interesting to get his perspective on some of the things John had learned-, but he quickly pushed that thought aside.

Elizabeth might be willing to accept such 'anomalies' as his Earth-like name and his presence in Atlantis, but Daniel Jackson's scientific insight into the Ancients might prompt him to ask too many questions that John couldn't answer.

His main strength right now was the fact that most of the people who knew about him assumed that he was an Ancient; if they knew just how comparatively limited his knowledge was, or if they knew how he'd really ended up in the city...

He wasn't sure what the result would be, but he didn't want to find out; his status in this city was hanging by an awkward thread at the best of times, and he wouldn't do anything to jeopardise that by making them think he wasn't the Ancient they believed him to be.

Right now, the only thing that he could do to help Earth was help to protect Atlantis from the Wraith while waiting for the SGC to find some kind of new information about wherever Merlin had hidden his weapon...

Still, if nothing else, they'd managed to destroy another Wraith hive during their efforts, while also destroying one of the Ori battleships that the SGC were dealing with back in the Milky Way galaxy; he might not like that he couldn't contribute much to that threat, but if he was able to help fight the Wraith, he could be assured that he was making a difference. He had his area of expertise, and SG-1 had theirs; some day a situation might arise that would require them to work together, but this wasn't that occasion.

Besides, as much as he wished that he'd had a chance to work with SG-1 during their time in Atlantis- they were basically legends, after all-, the rest of him recognised that he almost didn't want things to reach a point where the situation was dangerous enough to force him to make official contact with the SGC's primary team...

Shaking his head to force such thoughts away, he turned around and walked back into the service tunnels, leaving the archaeologist and the thief to their conversation; Elizabeth wasn't likely to show up any time soon, and he didn't have anything he could usefully say to them anyway.

* * *

AN 2: Short, I know, but I thought that it would be interesting; trust me, things are going to get much more difficult when Lucius shows up in the next chapter...


	30. Rejection

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: I give you my rewrite of 'Irresistible', which I hope will meet with everyone's approval; it starts promptly, and it probably won't be my longest rewrite, but things are going to become a bit more violent than they were originally...

Mystery of the Phantom

"Everything good?" John asked as Elizabeth walked out onto the balcony, smiling at her as he hopped down from his position above the door to join her.

They'd not had the time or opportunity to talk for a while, but with Atlantis's recent project focusing on their attempt to find 'spare' Stargates for the proposed inter-galactic gate bridge, there hadn't been much that John could usefully contribute to the project; he'd suggested that Elizabeth ignore a couple of gates without stating why he thought they should be ignored- he didn't want to lose access to his emergency supplies, after all-, but that was the extent of his involvement in it.

"Reasonably well for us, thanks," Elizabeth replied, smiling back at him. "We're making good progress finding gates for the inter-galactic bridge at our end, and apparently things are going... fairly well in the Milky Way as well."

John knew enough about the reports from the Milky Way to know that the search for Merlin's weapon had taken a dead end, but that wasn't important right now; there was nothing that he could contribute to that particular search, so pressing Elizabeth about the details wouldn't accomplish anything.

"So... what prompted this?" John asked, casually indicating the balcony. "Not that I don't mind the chance to chat, but... well..."

"I just wanted to ask you about something," Elizabeth clarified, saving him from actually voicing their 'unspoken agreement' not to discuss their lack of non-mission-related interaction; as much as John liked to think that Elizabeth would like to spend time with him outside of these meetings, putting her on the spot about the issue would have just felt awkward at best, given that there were few opportunities for them to spend time together that wouldn't have put John at risk from Sumner's military officers, particularly after the colonel's interest in the Phantom had increased following his last appearance. "We just received reports of an individual called Lucius Lavin on the last planet that Sumner's team visited, and he's apparently rather highly-regarded by his people and some other planets he's visited for some skills in exploration and medicine; he didn't exactly strike Sumner as authentic, but I wondered if you'd heard of him?"

"Name doesn't ring a bell," John replied, shrugging apologetically. "Still, keep in mind that I've been out of the loop for the last few years; maybe he's made an impact on things while I've... been away?"

"That's possible," Elizabeth confirmed, nodding in acknowledgement of his point, neither of them mentioning exactly _why _he'd been confined in his ability to make a greater galactic impact over the last few years. "Doctor Beckett's talking with him at the moment, just in case there actually is anything to his claims; he might be coming back to the city if the meeting goes well, so maybe you'll have the chance to meet him then."

"_See _him, anyway," John pointed out, smiling slightly at her, even as he felt a slight automatic tension in his shoulders at the thought of talking to anyone else outside of Elizabeth in such a casual manner.

He knew that it maybe wasn't a healthy response, but he'd spent so long hiding away from the rest of the city's inhabitants, save for when there was some crisis or another to deal with that required his direct intervention, that he just... didn't feel comfortable talking about interacting with someone in a purely social environment right now (Probably because the last couple of socialising opportunities he'd had with people ended with them chasing him away in a panic after they saw what was under the mask); Elizabeth was the exception only because he'd spent so much time talking with the body of her other self...

Shaking such morbid thoughts off, John jumped off the balcony, opening his cape so that he could glide down to his destination; it wasn't like he could complain about things in Atlantis being quiet, after all...

* * *

As he observed events in the city the following morning, John wondered if he should be concerned or just somewhat puzzled.

The news that Beckett had actually brought Lucius Lavin back to Atlantis had been a bit of a surprise, of course, but if McKay didn't prove that sometimes arrogance was deserved John didn't know who would prove such a thing; the man might seem a bit cocky from what he'd seen from his occasional glimpse of the new arrival, but after confirming that he wasn't carrying any weapons John had just settled down in a small compartment near the gateroom to keep an ear out for any potential developments after Sumner and McKay left to scout for new Stargates

However, when he woke up, he was left with the unnerving impression that something about the city had changed while he'd been asleep. It wasn't anything immediately obvious- Sumner and McKay were away, probably scouting out a few more gates, but that wasn't exactly unprecedented if they were checking out orbital gates were population contact was likely to be negligible, and everyone else seemed to be relaxed-, but there was something about the atmosphere that didn't seem right.

Granted, it wasn't like he spent a lot of time observing the fine details of everyones' daily activities in Atlantis, but he was fairly sure that the general staff should spend a bit more time perusing Atlantis's databanks and slightly less time gossiping about the new arrival... and when did a bunch of highly trained military operatives- particularly those commanded by someone as efficient and focused on the rules as Colonel Marshall Sumner- indulge in this much 'gossip'?

Maybe he was just being overly paranoid- with _Orion _in orbit and the drone weapon batteries fully stocked up, Atlantis was pretty much in the best condition it had been in since they'd arrived; the only thing they really needed that they didn't have was a few extra ZPMs, and the one they were using certainly had enough power to help everyone feel comfortable-, but that didn't stop John from feeling like he was just waiting for the other shoe to drop in this latest turn of events...

When he saw Elizabeth starting to walk towards their balcony, he was almost relieved at the possibility that he would get the chance to ask her a few questions; the way she was looking over her shoulder was a little unusual, but it wasn't like she wasn't allowed to be looking for someone else...

As he took up his position on top of the balcony, his smile brightened as Elizabeth walked out onto the balcony below him, but when a slightly overweight man with slightly receding curly black hair and dressed in loose-fitting white linen clothes who could only be Lucius Lavin walked out on to the balcony that he knew something was wrong.

Even without the fact that Elizabeth _never _brought anyone else out to what he would always consider _their _balcony, as soon as the overweight man had walked through the door, his vision briefly turned green as the emergency energy shield systems in his mask flared into life, covering his eye sockets and extending over his exposed jaw and cheek to 'clamp' down around his neck.

John didn't stop to think; ignoring Elizabeth's obvious breach of their unofficially-established protocol in this situation, John leapt down from his position above the balcony and landed behind Elizabeth and Lucius, standing straight up as they turned to look at him.

"Oh my- the _Phantom_?" Lucius said, grinning as he looked at John, apparently unconcerned about the cold stare John was giving him behind the mask as he walked forward to shake the masked man's hand. "It's an honour-"

"Wish that I could say the same," John replied, folding his arms as he glared at the other man, the faint glow of green in the corner of his eyes confirming that he was looking at someone with more than a few secrets. "What are you doing to them?"

"John?" Elizabeth said, looking at him with a smile that was so sickeningly sweet John would have disliked it under any circumstances- Elizabeth could be kind, but the expression currently on her face was just _soppy_ in a way that Elizabeth should never be-, her expression shifting to confusion as she took in his defensive stance. "What are you doing; Lucius is a wise and kind man who wouldn't do anything to hurt us-"

"And you're _certain _of that after he's been here for a _day_?" John said, looking incredulously at her. "You kept Chaya under more intensive guard than this, and she _definitely _had something you needed, and don't even get me _started _on how paranoid Sumner's men are around me even after everything I've done for this city; there's no _way _you're thinking clearly-!"

The implication of that statement only hit him once it was out of his mouth.

Elizabeth _wasn't _thinking clearly...

And, judging by Sumner's uncharacteristic attitude, he wasn't acting like he normally would in such a situation either.

Which meant that Lucius was using something to influence how everyone in Atlantis was behaving towards him...

"What are you using?" John said, his gaze fixed on the other man with renewed resolution as his sudden theory became ever more certain in his mind.

"What?" Lucius said, looking at John in what could almost be taken as genuine confusion. "I'm not using-"

"_This _is an automatic system that serves as an air-filtration unit," John said, tapping a finger against his cheek to reveal the glowing green glow of the simple Ancient shield he'd incorporated into the mask. "It automatically activates to protect me from toxins if I find myself on a planet with a hostile atmosphere; the city's own air-filtration systems were good enough to deal with whatever you're using when I was at a distance from you earlier, but now that we're in close proximity, _something's _set my alarm systems off... and since Elizabeth hasn't been offworld since the last time we met, _she _can't have picked something up, so the cause must be _you_."

"What are you talking about?" Elizabeth said, looking at him with that sick devoted confusion that put John disturbingly in mind of a child who didn't understand why Daddy was upset with Mummy (The idea of something reducing _Elizabeth _to this kind of state just made him feel _sick_...). "Lucius wouldn't do anything like that-"

"You've known him for a matter of _hours_, Elizabeth; how can you honestly say what this guy would or wouldn't do?" John asked, glaring over at her. "I don't care _what _he's using, but I do know that you're better than this; you've known me for _two years_-!"

"And at least Lucius has been open enough to show me what he looks like," Elizabeth countered, glaring at John with a sudden coldness about her manner that hit John with a more devastating blow than any weapon ever could have done.

_Elizabeth Weir_ didn't believe in him...

Because of that chubby-

"_BASTARD_!" he roared, rational thought forgotten as he grabbed Lucius by the shirt, muscles trained and honed by years of fighting Wraith hauling the slightly overweight man through the glass windows that had so long preserved their privacy. Crashing through the window, John hurled Lucius to the ground, pinning the other man down with his own body-weight, only to hear the sudden sound of several weapons cocking around him. His rage momentarily quelled at the sound of the guns, John looked up to find himself staring down the barrels of several guns, a large quantity of Sumner's marines at the other end of them.

John wasn't sure who to curse more; himself for being so hot-headed as to attack Lucius in the first place, or Lucius for driving trained marines to the point where they were willing to shoot the guy who'd helped them survive the siege last year for attacking someone they'd only just met (Maybe he'd deserve some hostility under other circumstances, but the guy had barely been here a day and almost certainly had _nothing _to offer)...

"Uh... I surrender?" he said, holding his hands up as he quickly mentally deactivated his personal shield device; given that it was hidden on his back underneath his outer top, he felt comfortable assuming that nobody would find the device, but the last thing he wanted was for anyone to have reason to suspect that it was there and take it away from him.

"Take him to the holding area," Sumner's voice said, the colonel walking down the stairs from where he'd been apparently working in the control room, looking scathingly at John as he quickly searched his belt and removed his weapons. "I knew you were screwed up, but I didn't think you'd fall so low that you'd attack _Lucius_."

John tuned out everything that Sumner was saying to him as he stood there in silence before he was taken away down the corridor leading to the holding cells; right now, all that he was focusing on was the look of disappointment on Elizabeth's face as she stared at him.

Disappointment at the fact that he'd _attacked _someone who'd turned the most incredible woman he'd ever known into a simpering fangirl...

He'd always assumed that he couldn't hate anyone more than the Wraith, but Commander Kolya had proven that theory wrong, and what Lucius had done to Elizabeth had pushed him so far up John's hit list that he was surprised he hadn't accidentally subconsciously ordered Atlantis to destroy the guy already.

Right now, he was going to give Lucius a chance to relax, work out what he was using, and then...

John fought the urge to smile at the thought of what he would do to Lucius once he had established what the other man had done to those he had sworn to protect.


	31. Breaking the Habit

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Another individual will get a glimpse at what is hidden under the Phantom's mask in this part of the story, but you'll have to wait until the right moment for a more detailed description; the audience will only get the full answers when Elizabeth does (But I DO have plans for her to learn some useful information soon...)

Mystery of the Phantom

Sitting in the cell that he had used to hold so many Wraith captive- back in the days when he'd been in control of the city and when he'd actually thought that they might give him information; it hadn't taken him long to work out that they'd never give him any information in the early days of his 'career' here in Pegasus, and after he'd established his reputation as the Phantom he'd become more concerned that the Wraith just wouldn't take him seriously if he had to ask them for help-, John couldn't believe it had come to this; after all of his efforts to remain free and avoid stirring the nest, he'd gone and completely lost it because of some fat git?

Still, as he took in his surroundings, he supposed that it could be worse. The fact that his mask still registered traces of whatever Lucius had been using on it at least ensured that the shield he'd included in the mask had prevented anyone from taking it off, and he still had enough weapons hidden in his cloak if he needed to break out, but that still left him with the problem of working out how to deal with the Lucius situation...

He might be a veritable genius when it came to dealing with ways of fighting the Wraith, but as his recent experience with Ford had forced him to recognise, he also suffered from the notable handicap that his area of expertise wasn't that useful when dealing with a threat that he couldn't just pummel, shoot, stab, or otherwise defeat using physical methods; he hadn't been able to do anything for Ford's mutating physiology, and even if he could identify whatever Lucius was using to trigger this bizarre cult-esque reaction in everyone around him, he had little hope that he could figure out a cure before anyone did something that would get them killed or that they'd regret when it wore off-

God, he shouldn't have allowed his thoughts to go there; all he could suddenly think of was the image of Elizabeth fawning sickeningly over Lucius, the arrogant git content to treat her as another conquest, with no understanding of just how incredible or precious she was beyond her ability to satisfy his pathetic physical desires...

He'd witnessed Wraith feeding, felt like his insides were trying to tear themselves apart when he'd accidentally overdosed on Wraith enzyme in a crisis and had to make himself go 'cold turkey' to get back to normal, seen bodies of the dead and dying in places where the Wraith had carried out more direct raids rather than simply abducting people to feed on them, but the thought of Elizabeth... doing _it_... with that bastard accomplished something that John had long thought he'd managed to completely overcome; the urge to throw up in horror and disgust at the scenario facing him.

"Are you comfortable in there?" Lucius's voice asked, John looking up to see the other man walking into the room with a nonchalant smile as though he had every right to be treating Atlantis like it was his, not even bothering with guards when facing a prisoner of John's reputation (John quickly halted that train of thought; he was _not _going to start assuming people should fear him without seeing him in action, and in any case Lucius's apparent under-estimation of John- or his own overconfidence in whatever he was using; either could account for what he was doing right now- would work in his favour at the moment).

"Fine, thanks," John replied, glaring back at Lucius as the other man casually stood in front of the cell. "So, now that we're alone, care to share what's _really_ going on here?"

"Can't we just talk?" Lucius asked, smiling at him with a smile that gave the impression of a man who was unaware of just how bad he was at dealing with people. "I mean, OK, it's terrible that Elizabeth had to do this, but here we are, two legends-"

"You're not a legend; you're just a potentially legendary git," John interrupted; he refused to be compared to this prat in any way. "And if you're hoping to win me over with whatever you're using now that we're alone, I designed my mask to cope with far more toxic and dangerous substances than something this fundamentally passive; we could be face-to-face for decades, doing _nothing _but talking, and you'd die of old age before my mask's systems were low enough on power to let that stuff affect me."

"Oh," Lucius said, sighing slightly mournfully as he looked at John. "Too bad; having you to help them would _really _make this easier..."

"Make _what _easier?" John asked, glaring at his adversary in exasperation, ignoring the slight tinge of fear he felt at Lucius's words; the idea that this self-centred git had a _plan _made his actions all the more a cause for concern. "What are you actually trying to _do _here?"

"Well..." Lucius said, looking contemplatively at him for a few moments before he shrugged. "You know what, I'm a good sport, and you've done a lot for us over the years; you can know my secret."

"I'm honoured," John said dryly. "So, what is it?"

"It's a herb, originally," Lucius explained with a proud grin. "One of my greatest discoveries... well, it's my _only_ great discovery, but you've got to admit, it's pretty great."

"What were you before it?" John asked, refusing to voice his thoughts on the herb; as far as he was concerned, the stuff was clearly an abomination that should have been destroyed before it could ever be used in this manner.

"I was a baker," Lucius replied with a shrug. "Bread, mostly; the occasional muffin at festival time..."

"So this herb changed all that, right?" John asked, already piecing things together.

"Yeah," Lucius confirmed, chuckling as he pulled up a chair and sat down. "I baked it into my own bread after I found it during one of my travels- I like to experiment with my ingredients- and I noticed that people started to like me... well, hate me less, but pretty soon it became like. So I perfected a potion. It worked great for years..."

"'Worked'?" John repeated, raising an eyebrow as he looked at Lucius, grateful that the man was the chatty kind of bad guy; clearly his ego translated into wanting to tell others about his 'success' if they were mentally capable of understanding how it worked even if they wouldn't agree with his motives. "What changed?"

"The Wraith set up an outpost on the only planet where I could get the herb," Lucius replied, his expression slightly grimmer than before as he continued his tale. "I knew I could never go back there."

"Which is why you were interested in what we had to offer, right?" John asked, nodding thoughtfully as the full details of Lucius's plan slotted into place in his mind. "A trained city full of soldiers and scientists, with access to technology beyond anything you've encountered before... _more _than capable of getting to that planet and bringing the herb back, right?"

"I'm telling you, it's fate," Lucius said with a smile. "And everybody wanted to help, so I let them. See, that's the great thing about this herb. Nobody gets hurt. They just want to help me all the time. What's wrong with that? I'm a nice guy; I never make them do anything they didn't wanna do."

"Don't you have six wives?" John asked, recalling something he'd heard one of the soldiers mention while he was being taken to the cell.

"Sometimes all at once," Lucius said, still smiling at the memory.

Only the fact that he'd already lost his control where this man was concerned once too often already stopped John from voicing his reaction to that; he had nothing against what people got up to sexually in their private lives so long as they kept it private, but the idea of Lucius using his 'powers' like _that_... basically abusing the herb's power to commit what essentially amounted to date rape and thinking that it was _acceptable_...

Then he remembered the manner in which Lucius had reacted to Elizabeth's presence, and John knew that his control was about to snap; the thought of this man treating Elizabeth- Doctor Elizabeth Weir, the woman who'd given up her life and any future she might have had to save this city- as though she was just another conquest had been bad enough, but the idea that he could feel _proud _about essentially _raping _someone...

The fact that he was willing to turn Atlantis into his personal slaves just to pander to his own ego would have been enough to earn John's enmity; the fact that he was basically talking about adding Elizabeth to his personal harem just made it all the more personal.

"The second that this force field comes down, Lucius Lavin, you are going to regret everything that you have done in this city," John said coldly.

"Oh, really?" Lucius asked, smiling nonchalantly at him.

"Really," John replied, staring grimly at Lucius. "I'm going to give you the benefit of the doubt by assuming that you're just a bit of a git rather than an absolute bastard and give you one last chance; let me out of this cell, leave this city, stop using that herb _anywhere _in this galaxy or any other, and I won't show you why I'm the thing that gives the Wraith nightmares."

"Why should I do that?" Lucius replied, still smiling at the caged Phantom. "You can't get out, and like I said, I'm not hurting anyone; they're not doing anything they wouldn't want to do-"

"Their judgement is _seriously _impaired by your influence, you fat bastard; they'd _never _go this far for something so goddamn _useless _as that herb if they were thinking clearly," John interrupted; this man practically spewed crap from both of his major bodily orifices, but that didn't mean he had to listen to it. "You want to send them into hostile territory-"

"I've just got them going to a planet which has a few things that might be useful; the fact that the Wraith are there is unfortunate-" Lucius began.

"The only thing that planet has is a single herb that you're dependent on to have any kind of social life because you're such a complete git that you'd never even get anyone to give you the time of day without it," John interjected once again, glaring resolutely at the other man. "You're a goddamn bastard, Lucius; you were pathetic before you found that herb, and now you're a pathetic junkie who depends on that stuff just to get by in contemporary society because you _know _that you'd never get anyone to like you on your own merits."

"Seriously, what are you even going to do to me?" Lucius asked, chuckling slightly as he looked at him. "I mean, OK, maybe you're immune to the herb, but you're locked up in that cell-"

Fed up with listening to this man ranting about himself, John decided to bring out his secret 'shock weapon'; reaching up to his face, John casually removed his mask, holding it in his left hand as he stared firmly back at the former baker's sudden expression of terror at the sight of what was under the silver metal.

"OH MY GOD!" Lucius said, his eyes wide with terror as he looked at the face that had driven John to done the mask in the first place. "Y-you-you-you're-!"

"I am," John said, glaring back at the other man, for once grateful for the bad reputation his true face had given him.

It sucked when you wanted to socialise with others, of course- they were so busy acting on instinct to get away from what they thought he was that they never realised the anomalies in his behaviour that would contradict that theory-, but there were times when looking like this had its advantages...

"You know what I am and what those like me are capable of if riled up," he continued, his gaze still fixed on Lucius with the same cold intensity that had made even a few Wraith back down when they found themselves facing it, slipping the mask back into place as he walked up to the cage wall to fix his adversary with the full intensity of his stare; the face was good for shock value, but if he was making conversation it was better to keep the mask on so that he could ensure that people were looking at his eyes rather than the rest of his face. "Either you let me out now, or things are going to get _really _unpleasant..."

For a moment, John just stared at Lucius, the other man looking at him with a wide-eyed expression of terror as his gaze remained fixed on the mask, clearly remembering what he'd only briefly witnessed underneath it, until he seemed to collect himself, his expression going from fear to self-satisfaction as something apparently occurred to him.

"You can't do_ anything_ to me!" he said, laughing with the kind of exaggerated laugh that was always used when the subject was trying to convince themselves that they had been foolish more than they were trying to convince others. "You're locked away in that cell for good, and these people are better off with you staying in there before you go and do what your kind always does; I'm going to make sure Doctor Weir knows-"

Lucius didn't even get the chance to finish his sentence before the cage suddenly deactivated, followed by the door opening as John charged out of the cage with such speed that Lucius was lying on the ground with John's legs on either side of his waist and his arms pinned by John's hands before he'd even had time to register that John had moved in the first place.

"That's the thing about my reputation," John said, smirking slightly at Lucius as though they were merely continuing an earlier conversation despite Lucius's obvious terror at their current positions. "People see the face or the gun or the sword or other relevant weapon and they assume that all I am is a thug who goes around hitting or shooting people a lot, and those who see my face _really _underestimate what I can do; it never occurs to them that, for example, I could have the intelligence to take precautions against the possibility that someone would lock me away in _my _city and try to use it against me."

"B-b-but-!" Lucius began.

"Oh, I know that my 'kind' are normally just driven by instinct no matter what everyone tries to teach them," John said, staring mockingly at the man below him- there were times when the false impression his face gave could be useful, even if he generally resented the reaction it provoked-, quickly patting over Lucius's clothes for a few moments before he pulled out a small glass phial, "but consider this; there must be _something _different about me compared to the others if I survived this long, right?"

He smiled as he waved the phial in front of Lucius's face. "This is that potion you mentioned, I presume?"

Lucius's panicked eyes widened momentarily at the sight of the phial, giving John all the time he needed, prompting him to stand back up and haul Lucius to his feet before throwing the other man into the cage, slamming a hand on the nearby control panel to shut it before he turned around to face the man as the cell walls sprang up.

"What-?" Lucius began, his eyes widening as John tapped at the cell controls. "What are you doing?"

"Keeping you on lockdown for the next day or so until I can render that herb of yours useless," John replied with a smile as he stepped back from the cell door. "The cell has its own air filtration system- one _completely _independent of the rest of the air in Atlantis; let's just say the Ancients designed this as a quarantine area as well as a jail cell-, so you'll be totally dependent on what everyone else has soaked up so far if you want to influence anybody, and I've just activated a little security program which keeps the lock on a rapidly-rotating combination control code that will only let you out when twenty-four hours have passed; could have left it for longer, but no matter how much of a jerk you've been, starving you to death is... well, it's not something I'm interested in doing."

"_WHAT_?" Lucius screamed, slamming his hands against the cell before he stepped back from the force field, his hands burned by the energy field. "But- but I'll-"

"Don't even think about claiming you'd starve anyway, you useless lard; you've probably grown used to eating to excess, but you've got enough extra weight around there that your body'll cope without food for a few hours, and you could stand to lose a few pounds anyway," John countered, glaring at the man on the other side of the barrier with a cold intensity that felt like John was preparing to bore a hole in the other man's head if he stared with any greater intensity. "This is Elizabeth Weir's city, Lucius Larvin; she has given more of herself to save Atlantis than even she knows, and I will _never _allow you to turn her into your fucking puppet because you can't accept the fact that you're a useless piece of _shit _who will never amount to anything or accomplish anything useful in his sad, pathetic excuse of a life."

"I just want-!" Lucius began.

"You _want_ nothing more than an opportunity to prove to yourself that you're something more than a useless load that nobody will ever give a crap about as himself, and I'm in no mood to even think of humouring you after what you've done," John countered, staring at Lucius for a moment before he sighed and stepped back. "However, right now, my priority is getting my weapons back and getting everyone else in this city back to normal; you'll be fine in there until I'm finished."

"Y-you can't _do _that!" Lucius protested. "I'll _starve_... you're the _Phantom_; you don't hurt humans-!"

"Firstly, as I already said, you _won't _starve, and secondly, you attempted to seduce the _woman I love_; do you really think I give a dead Wraith's useless kidneys about your physical comfort?" John spat (He cursed himself for revealing such an intimate detail to this git, but quickly pulled himself together; he hadn't exactly _confirmed _that it was Elizabeth he was referring to, and Lucius had certainly been flirting with enough of Atlantis's female population that it would be hard to identify who he was specifically talking about).

As satisfying as it would have been to threaten this bastard, he didn't really have time for this; Lucius wasn't going to leave of his own accord, and, regardless of how tempted he was to give in to his urges, John wasn't going to start mutilating someone for being a git.

"Enjoy your time in Atlantis," John said, smirking at Lucius as he stepped back from the cell. "I'll see you once I'm done."

"You _can't_-!" Lucius protested.

"I just did," John replied, sweeping his cloak around himself in an excessively dramatic flourish before he headed for the corner and vanished into the shadows, leaving Lucius to stare after him in shock at what he had just witnessed.

He'd worry about how everyone would react to this turn of events later; right now, he just had to hope that whatever Lucius had done wouldn't take _too _long to wear off to a degree that would make others willing to listen to him.

If he had kept track of the expedition's schedules accurately, Doctor Beckett _should _be in his lab carrying out a few searches of the Ancient database on his own; that meant that all he had to do was get there in the next few minutes and keep him on lockdown...

* * *

As he sat in one of the maintenance tunnels just outside of Doctor Beckett's lab an hour or so later, patiently waiting for the right moment to act, John was already wondering if this was the smartest move.

Getting Beckett on his own wasn't actually that difficult- with everyone fawning over Lucius, there hadn't been any missions that might require his attention if they came back suddenly, and Beckett was known for working on his own in the lab if he was particularly caught up in some experiment or another-, but the question was whether Beckett would even believe his 'story'; he'd had to come up with a basic story that didn't 'incriminate' Lucius that Beckett would hopefully listen to rather than focus on protesting Lucius's innocence, but if the doctor still wouldn't believe him...

Then, as he saw the last doctor leave the room, John seized his chance; exiting the maintenance tunnel, he slammed his hand against the nearest door control panel before Beckett could react to his presence, his decade-plus of experience learning how to control Atlantis's more subtle technology allowing him to put the entire lab on a lockdown that nobody else could hope to unlock without his permission.

"What- _Phantom_?" Beckett said, looking at John with a sudden panic. "What are-?"

"Doctor Beckett," John said, looking at the Scottish doctor with a slight edge of desperation that he hoped would reinforce the impression he was trying to create, "I'm sorry to bother you, but... I need your help."

"My help?" Beckett said, looking at John with new uncertainty. "With what?"

"I'm... I'm not feeling too well, Doctor," John said, taking the phial out of his pocket and showing it to Beckett. "I've been exposed to... well, I've been exposed to something and I've managed to collect a sample of it; I wondered if you could help me isolate it?"

"You... you think this is the reason for how you reacted earlier?" Beckett asked, looking at John with a slight smile.

"Well, that's... possible," John said, shrugging slightly as he tried not to smile too visibly; by creating the idea that _he _thought there was something wrong with his recent actions, he'd make Beckett more willing to help him. "I've got some ideas about what it will do, but I'd appreciate a more experienced opinion..."

"Of course," Beckett said, smiling reassuringly as he pulled up a nearby computer and scanner and began to analyse the phial's contents, staring contemplatively at the screen as further information was displayed before them. "Fascinating..."

"In what way?" John asked, trying to sound as eager as the others; judging by the way others reacted to Lucius's presence, the more eager he appeared right now the better.

"It looks like this phial contains a chemical that interacts with the human body to trigger pheromone secretion," Beckett explained, thoughtfully studying the read-outs on the screen in front of him. "According to this, it triggers the release in the prefrontal cortex, stimulating positive emotions relating to a particular person..."

"OK, so we've got what it does; is there any way to stop it?" John asked, hoping that Beckett's drug-addled mind wouldn't register the anomaly of the scenario described; how would a drug like this have provoked John to attack Lucius in the first place?

"Well, I _might _be able to develop a means of suppressing this reaction in injection format-" Beckett began.

"Is there any way we could add it to the city's air circulation?" John asked on impulse. "I mean, if it can affect me without my knowing it, maybe it could affect other people; shouldn't we get this spread out as soon as possible before anyone else can fall victim to it?"

"Well, possibly..." Beckett said, looking thoughtfully at him. "But shouldn't we let Lucius know that you didn't mean to attack him-?"

"We don't have time to ask his permission, and I'm sure he'll understand; just get the cure added to the system, Doctor Beckett," John said, staring firmly at the Scottish doctor while trying to restrain the urge to argue with him about his attitude towards Lucius; given the effect that the herb could have on him, he'd probably start protesting against John's suggestions if he started to imply anything that could be interpreted as acting against Lucius. "_Please_."

After a momentary silence, Beckett nodded.

"Well..." he said, shrugging slightly as he looked at the masked man with a smile. "You've done enough for us over the years... if this gets you back to normal, I suppose you're entitled to a break."

As the Scottish doctor started to work on the cure- from what John could see of the other man's work over his shoulder, it looked like the cure was relatively straightforward; all he needed was the right combination of drugs to regain control of the brain's pheromone secretion centres so that they could regain their control-, John mentally planned out his next move.

With the lab on lockdown and no way for sound to get through the emergency force field he'd erected around the door, there should be no way for anyone to interrupt Beckett's work; once they'd added the cure to the base's atmospheric sensors, it should only be a matter of time before the rest of the population were cured of their 'obsession' with Lucius. After the cure was added to the air system, he could leave the lab through the emergency tunnels and stay in hiding until the cure had taken effect; after that...

John didn't know; after what Elizabeth had said to him, the implications of doubt in him because he wouldn't show his face...

After he'd spent so long believing that she believed in him, just the _idea _that she had that kind of doubt in him on some level (The drug might people react positively to Lucius, but it couldn't create negative feelings against others)...

He needed some time to himself to think about _that _issue; as much as he wasn't comfortable thinking about her possible reaction, maybe it was time to think about showing her his face...

* * *

AN 2: As with the original episode, I'll be jumping to the aftermath of this event in the next chapter rather than actually showing Lucius's departure, as well as exploring how the events of "Sateda" go in Atlantis now that Sumner's the one in charge rather than John...


	32. Loss of a Runner

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: As mentioned, this takes place a couple of weeks after Lucius's departure, exploring the events of 'Sateda'- mainly from the perspective of Atlantis, but with further analysis of how Sumner differs from John as a commander-; hope you like what I have planned

Mystery of the Phantom

Looking out at the city, even after nearly two weeks since Lucius Lavin had 'visited' Atlantis, Elizabeth wondered if she would ever feel entirely clean again.

After she'd come so close to having sex with Lucius while under the influence of that... _herb_..., after she'd been willing to virtually hand control of Atlantis over to a man she'd only just met... when she'd been perfectly willing to-

Elizabeth didn't know if she'd ever lose the urge to throw up when she thought about what could have happened if John hadn't managed to act quickly enough to come up with a plan to create and disperse a cure throughout the city. She'd been hanging so keenly on Lucius's every ridiculous word... every pathetic story or flirtation that he had told had been met with a response that would have suited a simpering heroine from an old romance novel rather than the mature woman she was... and what she could have done with him if John hadn't locked Lucius away and risked everything to escape and find a way to devise a cure...

The look on Lucius's face when they'd hauled him out of the cell alone had almost made up for the humiliation he'd put them through, relief quickly giving way to terror as he took in the glares on their faces and was forced to realise that the drug he'd been using was no longer having any effect on them. With the cure having been released over Lucius's planet to help those village residents still in 'detox' from prolonged exposure to him- Doctors Beckett and McKay had found a way to use the puddle jumpers to spray the cure over the village in a liquid state-, Lucius had been returned to his planet, leaving him to make his own way on a world that would at the very least drive him off it once they'd completely recovered from the drug's influence.

She just wished that she could find it as easy to arrange a meeting with John to apologise as it had been for her to get Lucius sent away from the city he'd so nearly practically taken control of. She'd tried to wait for John on their balcony, but he'd never shown any sign that he even knew that she was there, to say nothing of the lack of evidence to suggest that he was in position to join her.

It was almost refreshing to have the city return to normal now; they'd spent some time engaged in mandatory counselling to cope with what they'd done under Lucius's 'control'- a policy encouraged among the Stargate program ever since Hathor's near-takeover in their first year-, but with immediate potentially traumatic reactions to the mind-control cleared up, they were now returning to their more traditional routine, as Sumner and his team investigated the next planet on their list.

Elizabeth wasn't sure what it said about her relationship with John that she wished some crisis requiring his attention would emerge sooner rather than later; she _had _to apologise for what she'd said to him while under Lucius's influence.

Maybe she sometimes felt frustrated that he didn't feel like he could trust her with the truth about what he looked like under his mask, but she did trust that he had a reason for wearing it- even if it was mostly just habit rather than anything else-, and respected his wish to keep the mask on even when they were talking on their own; if he'd just give her the chance to explain-

The sound of the Stargate activating drove her mind back to the present, prompting Elizabeth to glance at her watch; it was too soon for any offworld teams to be coming back, which increased the possibility that something was wrong. As she walked back into the gateroom from her balcony, she was greeted by the sight of an active Stargate, followed by McKay staggering through the event horizon before he collapsed to the ground as the gate shut down, revealing an arrow sticking out of his rear end.

If this had been any other situation, Elizabeth supposed that it would have been funny- the idea of someone being injured in their ass _was _kind of amusing, when you got down to it-, but she didn't have the time for that right now.

"Medical team to the gateroom!" she yelled as she activated her radio, before hurrying down to the gateroom to crouch down anxiously beside her chief scientist. "Rodney, what happened? Where are the others?"

"They're... right behind me..." McKay said, shaking slightly as he indicated the now-inactivate Stargate as the medical team ran into the gateroom, quickly moving into position around McKay as he collapsed to the ground, pain etched all over his features.

"Get him to the infirmary, and get him in a condition where he can talk," Elizabeth said, nodding at the relevant doctors as she stood up.

It might be an abrupt way to deal with this situation, but she wasn't going to get her military commander and her native Wraith experts back without more information about what had actually happened to them on the other side of the Stargate, and right now McKay was the only viable source of information that she had.

* * *

An hour or so later, Elizabeth stood in the infirmary- she'd thought about waiting on the balcony to attract John's attention, but had dismissed that idea fairly quickly; judging by the arrow that had injured McKay, the planet he'd visited wasn't populated by a particularly advanced race, which limited the possibility that it was a world that the Phantom would have paid significant attention to, and she couldn't exactly ask him to help her rescue Sumner without drawing too much attention to their association-, looking anxiously at McKay as he lay on the bed, Doctor Beckett and Major Caplan- Atlantis's current military commander in Sumner's absence- on either side of her.

"So many colours," McKay said, currently on a bed in the infirmary, his voice possessing a slightly sing-song like tone as he stared out at nothing in particular. "All the pretty horses."

"What's he talking about?" Elizabeth asked, looking anxiously over at her chief medical officer.

"I gave him some morphine for the pain," Doctor Beckett said.

"I need to know how many villagers," Major Caplan said, leaning down to look sternly at the Canadian as McKay weakly raised his head to look at the man addressing him. "How far is the gate from the village?"

"Have you seen a guy around?" McKay asked, raising his head to look uncertainly at the major, grinning vaguely as he spoke. "He looks like you, but he's got curlier hair and a squarer face... And... and a... and a pretty girl and a caveman..."

"I may have given him a wee bit too much, but he was making it impossible for me to treat him," Beckett said, looking apologetically at Elizabeth as he indicated McKay.

"Snap out of it, McKay!" Caplan said, glaring at the physicist in frustration. "It's important!"

Elizabeth might have agreed with Caplan's intentions, but she made a mental note to stop him if he tried to take this 'interrogation' any further; considering that McKay was fiddling with his nose at the moment, it was

"Come on!" Caplan said, as McKay reached up and appeared to be examining his own nose. "What kind of weapons did they have?"

"I'd say something that shoots arrows is a good guess," Beckett pointed out.

"Excuse me," McKay put in, his voice sounding more normal even if it was still obviously weaker than it should be. "Why am I lying here?"

"You have an arrow, Rodney," Beckett replied. "In your gluteus maximus."

"Oh. Well, that sounds painful," McKay said, sighing contentedly as he laid his head back down on the bed with a contented sigh. "Gluteus maximus. Glootus... maaxim..."

His sing-song tone was cut off as he turned his head drowsily, apparently having processed what part of the body they were talking about even as his vocal pace remained relatively slowed.

"Oh my God!" he said, his tone shocked even if his voice wasn't significantly louder than it had been. "That's my ass, isn't it?!"

"Aye," Beckett said, smiling slightly at McKay's recognition of what he was talking about.

"Call me when he's in a position to talk more clearly," Elizabeth said, turning around and heading out of the infirmary.

Hanging around here waiting for McKay to be stable enough to talk clearly wasn't going to accomplish anything right now but distract her from other things she might be doing with her time.

* * *

Sitting in her office as she went over some of the daily paperwork, Elizabeth wondered what it said about her relationship with her military commander that she was this calm about his continued absence from the city.

It wasn't that she wasn't worried about him, but she was almost more concerned about about Teyla and Ronon's continued absence than she was worried about Sumner's. Teyla and her had formed a bond since the Athosian had first come to Atlantis as the two most powerful women in the city- even if she didn't like to think that her rank made her 'better' than anyone else, it was hard for her to ignore the fact that she had authority over virtually everyone else in the city; she sometimes wondered if part of her friendship with John was the fact that she didn't have to order him anywhere-, and even Ronon provided an interesting insight into life in the Pegasus galaxy from a military standpoint that she found useful when drawing up new treaties for their allies in Pegasus, but Sumner...

Even as they entered their third year in the city, all that she could really say about her military commander was that he did his job; he didn't really _connect _with anyone in the city on a personal level, and didn't seem to be interested in changing it. He might be polite enough company, but he just continued to insist that he was maintaining a professional distance to do his job, regardless of the fact that they were in a situation where the ability to rely on each other in a crisis was all that they had to depend on, particularly given the distance between them and the nearest possible ally.

Still, no matter how uncertain she might be about Sumner, she couldn't deny that he did the job; it was the main reason that she'd never bothered to try and ask for someone else to take command of Atlantis's military contingent, given that she had no real reason to object to his actions even if he wasn't the most amiable of people.

She was distracted from her train of thought when the Stargate activated again, prompting her to get up and hurry into the control room as Chuck examined the control panel.

"It's Colonel Sumner's ID, ma'am," he said, looking up at her as she walked over to stand beside him.

"Lower the shield," she said, smiling in relief before she turned to walk down the stairs, only for the smile to falter as Sumner and Teyla were the only ones to walk through the Stargate, which subsequently deactivated with no sign of the third missing man.

"Where's Ronon?" she asked, looking at Sumner.

"Still being held on the planet," Sumner said, looking grimly at her. "He visited that world during his time as a Runner and the planet was culled as a result; the Wraith left the local population with instructions to capture Ronon and contact them if he showed up again."

"Ronon was able to arrange for Colonel Sumner and I to be released by threatening to cut his own throat if they did not let us go," Teyla explained, her hurried tone clearly reflecting her horror at the scenario they'd only just witnessed. "We must return to the planet and rescue him."

"Agreed," Elizabeth said, activating her radio. "Weir to Major Caplan; I need a team for a search and rescue mission to get to the gaterom immediately."

"_Understood_," Major Caplan said, terminating the connection.

"They are not a particularly advanced people in terms of weaponry, but they do have the advantage of numbers," Teyla said, looking at Elizabeth. "If we can move into action as quickly as possible, I believe that we should have time to rescue Ronon before the Wraith arrive; it took us fifteen minutes to walk from the camp to the Stargate, and if we move quickly we should get back there in slightly less time."

"Good to know," Elizabeth said, smiling gratefully at the Athosian woman's optimism, even as she already had a strong feeling that it wasn't going to be that simple.

The team might be on their way, but that still left the Wraith with a fair amount of time to 'collect' Ronon before they could get him...


	33. Rescuing the Runner

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: A bit of a quicker version than what happened in canon, but I think it works, particularly when the superior strength of the _Orion _is taken into account.

Mystery of the Phantom

"So," Elizabeth said, looking at Sumner and Teyla as the senior staff sat around the conference room table- McKay shifting slightly as though his wound was still hurting him-, "by the time you got back to the village, the Wraith had already managed to collect Ronon and cull the rest of the inhabitants?"

"All we found left of him was this," Sumner said, pulling out Ronon's distinctive weapon and laying it down on the table before him so that the others could see it. "There were a few dozen bodies lying around- enough to make it clear that the Wraith's claims to be willing to make a deal weren't worth crap-, but none of them Ronon's; there's no way to know if he's even alive-"

"He is," Teyla said.

"Don't get me wrong, I hope he is, but... how can you be certain?" Beckett asked, looking uncertainly at the Athosian.

"They made a sport out of trying to kill him in the past," Teyla said simply in response.

"And... because he got away, you think they'll try and finish the job?" McKay asked.

"They will try again," Teyla said grimly. "As we have seen, the Wraith do not accept defeat easily."

"But they have to acknowledge how dangerous he can be," Elizabeth said, looking solemnly at the rest of the people in the room. "It's not like they're going to give him a fair chance."

"Which means we have to work out a way of finding him," McKay said, smiling around the table before he restrained a slight wince at a fresh burst of pain from his injured rear. "And, if the Wraith have re-planted him with a tracking device like they did last time, we _might _be able to use the one we took out of him when we met him to tune the long-range sensors to pick up any similarly generated subspace transmissions..."

"You just came up with that?" Sumner asked, looking at him in surprise.

"I... had some time to think when I heard what had happened to him," McKay replied, shrugging slightly as he looked over at the colonel, the slight wince as he spoke the only indication of just how much pain he'd been in during that time.

"We _are _still assuming that the Wraith put a tracking device back in him," Sumner said, ignoring McKay's other comment. "They could have just killed him-"

"We _don't _leave our men behind," Elizabeth said, looking resolutely at Sumner before he could continue his speech. "Ronon has helped to defend us against the Wraith for over a year now, and he has _never _asked us for anything more than we were willing to give; after everything he's done for us, I think it's only fair that we try and save him, no matter how slim the chance might be."

She knew that part of her current defence was motivated by her concern for John- he might be more 'official' than John, but Ronon was rather similar to him-; it was possible that part of her was hoping that, if Sumner could be convinced to save Ronon, it would set a useful precedent for when he had to work with John again in the future...

* * *

"Sateda?" Sumner said, looking sceptically at McKay a couple of hours later, McKay having completed his analysis of the tracking device they'd originally extracted from Ronon and running that frequency through the city's long-range sensors to find similar signals being transmitted via subspace. "You're sure?"

"Well, there's a few other signals, but since one of the signals is from the location we've already identified as Sateda, I think focusing on that would be our best bet; Wraith aren't exactly complicated when it comes to this kind of thinking," McKay said, shrugging slightly as he looked at Sumner. "We've already checked and the Satedean Stargate's been taken off the grid for some reason; since the Wraith had left it alone the last time we tried to visit it, I'm guessing that whatever Wraith took Ronon felt like going 'back to the beginning' and stick him somewhere he'd make interesting prey while at the same time making sure he couldn't actually _do_ anything to escape them."

"Precisely," Teyla said, nodding in agreement at McKay. "Ronon is dangerous, but if the Wraith can confine him to one world, he will eventually succumb to sheer weight of numbers if nothing else."

"But, if there's no Stargate, than the only way for us to get there is by ship, which means that the only way for any Wraith to be there is if there is already a Hive ship in that location," Sumner said, looking grimly over at the rest of the people at the table. "I know that _Orion _has proven itself against hives in the past, but are you seriously suggesting that we take our strongest ship and most valuable asset all the way to a Wraith-controlled planet to rescue one man?"

"We don't even need to engage the hive if we don't want to," McKay pointed out. "We go to Sateda, beam him aboard, and then get out of there."

"You know that the Asgard transporters we've added to the _Orion _don't have the range necessary to beam Ronon to safety without us coming within visual range of the planet, which means we'll be within range of the hive-ship," Sumner said, looking grimly at the rest of the people sitting around the table. "I know that the odds are in our favour, but I am _not _going to put our best ship at risk for one man-"

"Who isn't a member of the US military?" McKay asked.

"That is _not _what I said-!" Sumner began.

"But it's what you're thinking, right?" McKay countered, glaring at Sumner. "Just because Ronon's not automatically obligated to play by your rules, you're going to just leave him out to dry when we have a _chance _of saving him?"

"Ronon Dex has been a valuable resource for the past year; if I could be sure of saving him-" Sumner began.

"He's one of us, Colonel Sumner," Elizabeth interjected, glaring at the military commander whose continued presence in the Stargate program was becoming increasingly inexplicable to her; not only did he seem to just regard it as another job rather than the most incredible experience in human history, but he appeared to have not even bothered to try and form the human connections that she'd come to expect from teammates during her time in command of the SGC. "We _don't _leave our people behind if there's any chance of survival."

"I acknowledge that, Doctor Weir," Sumner replied, looking back at her for a moment before he turned back to look at the other three people sitting around the table, only to be met with hard stares from Teyla and McKay and an equally firm glare from Doctor Beckett despite his own comparative lack of experience with Ronon.

"I'm just..." the colonel said, sighing in resignation as he took in the expressions facing him. "I'm just saying it's a very bad risk/reward situation; we have no way of knowing what we'll encounter when we get there and the _Orion _is still not quite back to its peak, even with the... additions you're including, to say nothing of the fact that we're still working out how to restore its power supply if we push it too far."

"So long as we can get to Sateda, we'll worry about the finer details when we have to," McKay said with a shrug. "The sensors are advanced enough that we can spot the Wraith long before they spot us, even without the other features we've added recently; if there's too many for _Orion _to handle, we'll take a cloaked gateship and head the rest of the way."

"I'll go with them, remove the tracking device before we get back on board," Beckett added before anyone else even had to suggest it.

"We'll be out of there before the Wraith even know what happened," McKay continued.

After a few moments of silent contemplation, Sumner nodded in resignation.

"Fine," he said at last. "Let's go... so long as you understand that we engage the Hive-ship only if we can be _certain_ of victory."

"With drones, Ancient sensors, and the element of surprise on our side?" McKay said, smiling reassuringly at the colonel. "We'll be fine."

* * *

As he lay on a bed in the _Orion _infirmary, McKay cursed his still-aching rear end; even after the time he'd spent working on the tracker that had been in Ronon's back, his ass was still aching where the arrow had struck him, which left him forced to endure further treatment to ensure that nothing had been missed.

"Son of a... you're _killing _me!" McKay said, wincing as Beckett continued his examination.

"I'm not even touching you," Beckett said, looking at the Canadian in frustration. "Seriously, Rodney, I've never treated a bigger baby in my life."

"Just... are we done?" McKay asked.

"Yes," Beckett said, stepping back and removing his gloves with a sigh. "It looks fine, considering."

"How is everything here?" Teyla asked, looking curiously at her teammate as she walked into the infirmary just as McKay had finished pulling up his trousers.

"Aside from Rodney's typical reaction when faced with pain, he's fine," Beckett said, smiling at the Athosian woman before he looked over at McKay. "Come to think of it, why are you here?"

"What do you mean?" McKay asked, looking at Beckett as he walked over to another table.

"On this mission," Beckett clarified, as he sorted through some of the material on the nearby table. "You're injured. You can't even sit down comfortably."

"Doctor Beckett is correct, Rodney," Teyla said, looking curiously at him. "People would not think less of you for remaining behind."

"What, you think I'm completely focused on what people think of me?" McKay asked, looking sharply at her.

"I did not say or think that; I am merely curious as to why you show this much concern to a man who is not of your world who you have spent so little time with," Teyla said, looking inquiringly at her teammate.

"Hey, I am a very caring person," McKay said, only to be met with stares from Beckett and Teyla. "OK, maybe it's not obvious to everyone, but, um..."

"You care about what happens to Ronon?" Beckett said, ceasing his examination of a sample in a microscope as he looked at his friend.

"Yes, of _course _I do," McKay replied indignantly. "What makes you think I wouldn't?"

"You have been known to refer to him as 'the caveman' behind his back; I do not believe that is an acceptable term to use when referring to a friend," Teyla said, looking sceptically at the physicist.

"That is a nickname," McKay replied defensively. "Buddies have nicknames for each other."

"You consider yourself and Ronon... 'buddies'?" Teyla repeated, looking at him in surprise as Beckett began to examine another sample. "Even though he is not of your world, and... I cannot recall; have you ever had a conversation with him outside of our missions?"

"That's... not relevant right now," McKay said, glaring briefly at her before he shrugged. "Anyway, we have an... unspoken bond; he's like a brother to me."

"Aye, a brother who got every gene you didn't, and vice-versa," Beckett said, looking sceptically at McKay.

"You know, just because Sumner being stand-off-ish is his way of making it hard to get to know _him _doesn't mean that the same thing applies to Ronon!" McKay said, glaring at the doctor. "I mean, OK, they both aren't exactly the chattiest of people, but they're not quiet for the same reasons; Sumner's quiet because of that screwy professionalism of his, and Ronon..."

"He is silent because he has spent many years alone," Teyla finished, smiling slightly at McKay as she thought about what he had just said. "You... truly are concerned for him, are you not?"

"Well, it's... you know..." McKay said, shrugging slightly, suddenly awkward about what he'd just been saying now that he'd been given a moment to reflect on it. "I mean, we've accepted you and the Athosians pretty well..."

"But that was when we had something to offer you on a larger scale," Teyla said, looking solemnly between McKay and Beckett. "While I never doubted that your intentions were good, there were practical motivations behind that decision as well as moral ones, to say nothing of... well..."

"The fact that Colonel Sumner never really seems to have moved on from considering you a local asset rather than a teammate?" Beckett asked, smiling reassuringly at Teyla. "Don't worry about it, Teyla; I sometimes think he mainly got the job of Atlantis military commander because he doesn't really connect to _anyone_, so it wasn't that much hassle to transfer him here because he wasn't leaving anyone behind."

"Yes," Teyla said, nodding slightly awkwardly at Beckett- clearly, even if he wasn't here, she wasn't entirely comfortable about essentially insulting Sumner behind his back, given that he had ensured their safety from various Wraith attacks even if he wasn't that easy to relate to- before she looked back at McKay. "Nevertheless, the fact that you are both this willing to protect Ronon is appreciated; Doctor Weir has always been accepting of me and my people, but it is... difficult... to know how you feel about someone who had spent so little time with you and done so little."

"He's been our friend," Beckett said, smiling politely but firmly at Teyla. "Maybe that's not enough for Sumner to want to mount this mission on its own, but it's enough for me."

"The point is," McKay said, coughing slightly to draw their attention back to him, as though uncomfortable with the emotional turn it had taken, "maybe Ronon and I don't talk much, but some things go deeper than words; the fact that some of us don't get that doesn't mean that it doesn't matter."

"Quite," Teyla said, smiling briefly at him before she turned to address both him and Beckett. "In any case... thank you for your concern."

"For Ronon?" Beckett said, smiling back at her. "No need to thank us, lass; all in a day's work, after all."

Teyla's simple smile in response to that statement somehow made it even better; she knew that there was still more to it than what they were willing to discuss, but what they had said was enough for the moment.

* * *

As they left hyperspace in orbit of Sateda, none of the Atlantis staff were surprised to see the now-familiar sight of a Wraith hive-ship hovering over the planet's surface, the occasional dart flying around it; at least they weren't trying to bomb the planet any more, even if that still didn't tell them where Ronon was.

"Where's the tracker?" Sumner asked, glancing over at McKay.

"On the planet," Chuck replied from his position standing over the science console, the technician having requested to come along on this mission for a bit of variety from his usal duties at the DHD. "There's a few Wraith life-signs around there as well, but Ronon seems to be OK."

"No other signs of Wraith ships?" Sumner asked.

"Apart from that one, this place seems pretty quiet Wraith-wise," Chuck confirmed, before looking curiously at Sumner. "Orders, sir?"

For a moment, as he stared at the hive-ship, everyone present wondered if Sumner was going to order them to withdraw and leave Ronon on the planet to cope on his own, his words about the practical value of this mission fresh in their memories, but then he nodded firmly as though coming to a decision.

"Battle stations," he said, moving over to sit down in the central command chair. "Prepare the drones and fire when ready; I want that hive-ship out of the picture before it knows what's hit it."

"Already on it," McKay said, smiling as he tapped a few buttons to activate the _Orion_'s new cloaking device, taken from one of their lost gateships and modified to suit the larger vessel. As with the similar measure used to install the cloak in Atlantis, it cost them their conventional shields and prevented them from using the Asgard transporters when it was active, but considering that they could still fire their weapons while cloaked so long as they were relatively close to the target, McKay's team had felt that the trade-off was worth it.

For the next few moments, the _Orion _advanced forward under the cloak, its engines on low power to decrease the likelihood of it generating any energy that the hive-ship could detect, until it finally came within close firing range of the larger ship with no sign that the Wraith were even aware that it was there.

"Picking up transmissions from the surface to the hive," McKay said, looking over at Sumner. "It looks like... a broadcast of some kind..."

"Wraith equivalent of reality TV?" Beckett suggested with a slight shrug. "Whoever's on there went to a lot of trouble to get Ronon back; they'd probably want to be sure that they saw him die, even if they decided to put him in an environment where he'd have a chance."

"It's nothing we need to see," Sumner said, looking firmly at the Wraith ship in front of their observation windows. "Fire all drones."

With that command, a spree of brilliant gold seemed to emerge from nothing and charge towards the hive at virtually point-blank range, tearing through its hull and easily obliterating the few darts flying around the ship before they could so much as turn around to start to fire at the area that was the source of this new attack. In a matter of moments, the hive had been torn apart, _Orion _converting the cloak back into a physical shield and pulling away as the ship exploded behind them, soon leaving nothing but a few small pieces of debris to show that it had ever been there.

"_Nice_..." Chuck said, smiling at his first sight of what _Orion_ was capable of.

"Don't get used to it," Sumner said, looking firmly over at the young technician.

"Sure," Chuck said, nodding in subdued understanding at Sumner's meaning; _Orion _might be powerful, but its drone supply was limited, and it would still be vulnerable if subjected to a sufficient number of opposing ships.

"Lock on to the tracker and beam Ronon aboard," Sumner said, nodding grimly at McKay before he activated the radio. "Doctor Beckett, Ronon Dex will be on board soon; prepare to operate as soon as possible."

"_Understood_," Beckett's voice replied.

Even as Sumner was speaking to the doctor, McKay had already returned his attention to the control panel for the Asgard transporters, tapping a few key switches before he looked back at Sumner with a smile.

"Done," he said with a reassuring grin. "See what I meant about it not being difficult?"

"Just remember that we can't afford to get complacent," Sumner said, looking pointedly at McKay. "We were lucky this time, but this ship still only has so many drones available to it; if it wasn't for the fact that we were almost certainly only going to be dealing with one hive-ship, I wouldn't have agreed to this."

"Understood," McKay said, nodding briefly at the colonel.

"Good," Sumner said, before he activated his radio. "Doctor Beckett, this is Colonel Sumner; how's Ronon?"

"_Uh... about what you'd expect_," Beckett's voice replied. "_He looks like he's been through the wars- taken quite a battering, got a few injuries that are going to need tending to, and collapsed while yelling at me about the fact that he hadn't killed all the Wraith yet-, but the fact that he felt comfortable enough to fall down should probably be a good thing_."

"_We have given him somewhere where he knows that he will be safe_," Teyla's voice said, sounding satisfied with the result. "His reaction... will be dealt with when he is safe."

"Quite," Sumner said, before he shrugged and turned his attention back to the rest of the crew. "Take us back to Atlantis."

"Understood," Chuck said, nodding briefly at Sumner before he activated the required controls, turning the _Orion _around to head back towards Atlantis.

_Orion _may be more practical as a secret weapon rather than a regularly-used tool for their arsenal, but it had certainly proven its worth on this occasion; another hive-ship had been destroyed, and Ronon was safe.

* * *

AN 2: As I said, a simple conclusion, but I feel it works to establish _Orion_'s role in this reality; a secret weapon to be used only when necessary to ensure its secrecy and preserve its power supply and weapons, since they can't guarantee that they'll be able to recharge or restock it.

Coming up next, a certain crisis that will end up being far more personal for Elizabeth than anyone could have expected...


	34. Pre-Mission Reflections

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This chapter is relatively short, but it's mainly intended to foreshadow the next one; hope you like it

Mystery of the Phantom

Elizabeth was almost afraid to jinx it, but she had to admit that the last couple of weeks had gone by relatively smoothly.

Not only had they successfully recovered Ronon and destroyed another hive-ship, but the next few offworld missions had all been relatively straightforward ones as well; a few close calls with a couple of less welcoming natives than they had anticipated, but it was never anything to the same extent as what they'd dealt with prior to Ronon being captured, and they'd managed to make a few potentially useful alliances in the process.

Admittedly, relations between Ronon and Sumner were slightly strained- the former Runner would have preferred it if Sumner had allowed him to eliminate the Wraith commander himself, and resented having that chance taken from him-, but it wasn't anything more serious than what their dynamic had been before the abduction; as long as the two of them were still able to work together, Elizabeth didn't feel the need to try and mend fences that hadn't made that much of a difference when they were there.

Besides, with their latest discovery about what was on the other side of the Stargate address they'd just discovered in the database, Elizabeth had more important matters to think about...

"Hello," said the voice that Elizabeth had been waiting to hear for longer than she liked to remember, prompting her to turn and smile at the sight of the masked man standing behind her.

"Hello, John," she said, smiling warmly at him, unwilling to think too much about what she'd said to him in their last meeting; that part of their lives was over now, and she could only hope that John knew that she would never judge him for wearing a mask around her.

"Nice job with Ronon's rescue last week," John said, smiling in approval at her as though his silence from the last few weeks had never happened. "Good to see the _Orion _pulling its weight."

"We wouldn't even have been able to accomplish that much if it wasn't for your contribution," Elizabeth said, smiling gratefully at John before another thought came to her. "I don't suppose you...?"

"All I know about the _Orion_-class's power source is that they rely on a slightly lower-grade ZPM in the engine core; I can't give you any more than that," John said, looking apologetically at her. "I've had a lot of time to study the database, but certain parts were always easier to follow than others; working out how to fix some things was easier than working out how to build something from scratch."

"Talking of the database," Elizabeth said, looking curiously at him, "how come you never visited this colony?"

"As you've observed yourself, all the database said about it was that it was the site of an abandoned Ancient experiment," John replied, shrugging slightly. "I didn't have any means of checking out what the colony was like without going through the Stargate myself, and it was too far away for me to visit it with my hyperdrive-capable... gateship; even if I'd taken the ship to another 'gate and travelled to it from there, it was too far away for me to feel comfortable checking out a planet that could have been turned into a radioactive husk or something like that."

"That's... a bit negative, isn't it?" Elizabeth aside, looking uncertainly at the man in the mask.

"When it comes to the Ancients, I find that, when they admit their errors, it's best to assume the worst," John said. "I may live in their city, but I'm not blind to the mistakes they've made in the past; I didn't see the point of risking a trip to a potentially dangerous planet just to find another way they'd possibly screwed up."

"But now that you know what it is..." Elizabeth asked.

"Give it a shot," John said, smiling at her. "Anything involving apparently live Ancients is _definitely _worth you paying them a visit."

"Good," Elizabeth said, nodding at John.

It wasn't that she would have cancelled the mission if John hadn't approved of it, but it was good to receive confirmation from her greatest available Ancient expert that this mission was worth her decision to take a rare personal trip through the Stargate.

If all went well, they'd be coming back to the city in a few hours with a new alliance with some _very _powerful allies...

* * *

AN 2: As I said, short, but the next one's going to be more interesting, as we enter the events of a VERY particular 'Atlantis' episode...


	35. The Real World

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This begins shortly after the end of "Progeny" before leading into "The Real World"; hope you like it.

As always in these cases, what I don't specifically record happened essentially the same way that it did in the show and will be referenced appropriately, although changes have been made that you'll notice when the time comes; I had a few ideas that I had to include

Mystery of the Phantom

Looking out at the city before her, Elizabeth found it hard to fully believe what she'd just been through.

After all of the times they'd wished that they could find Ancients who had never Ascended, their most promising lead ever had turned out to be a group of deranged early human-form Replicators who couldn't accept the rejection of their 'parents' and had subsequently attempted to destroy the entire city of Atlantis just to eliminate them.

She supposed they should consider themselves fortunate that Ronon had come along; even with McKay's attempt to hack the Asuran network, everything they'd done to try and escape would have been worthless without the temporary advantage provided by Ronon's gun.

Elizabeth ignored the part of her mind that noted that the weapon's use in a fight at least meant that John would be able to fight the Asurans if the situation called for it; she didn't want to _have _to rely on him for everything, even if she appreciated the fact that he was always there when she needed him (It was one reason that she was doing this rather than writing her reports; she wanted some time to think and put everything in its proper context, rather than run the risk of relating something back to John).

Besides, hadn't today proven that she didn't need to fall back on John for help whenever things became unpleasant? She might have been nearly strangled by Niam, but that was only because of some last-minute modifications that Oberoth had made to his programming; prior to that unfortunately turn of events, she liked to think that the team had everything under control, with the Asurans defeated, their city-ship destroyed, and their attempt at a direct assault averted...

* * *

As she opened her eyes and looked up at her new surroundings, Elizabeth didn't understand what had just happened.

One minute she'd been on the balcony of Atlantis in her uniform, thinking about what had just happened, and now she was lying on a bed in a white room that she'd never seen before, dressed in loose white clothes that put her in mind of something that a patient in a hospital would wear, with a simple plastic chair and a blue blanket-coloured bed the only sign of furniture. The sound of an ambulance outside startled her, but not nearly as much as when her attempt to look out of the sunlight-illuminated window covered by a conventional venetian blind revealed a brick building that was clearly nowhere on Atlantis.

Retreating from the window in shock, Elizabeth glanced down at herself once again, and this time noticed a plastic medical bracelet around her wrist. Glancing at it failed to reveal any clear information- apparently the old joke about the illegibility of doctors' handwriting was accurate in this case-, so, with nothing else available for her to do, she turned to the door of the room, but an attempt to open it quickly revealed that it was locked, and her look through the window in the door revealed nothing more than a corridor on the other side that looked far more appropriate to Earth than Atlantis.

"Hello?" Elizabeth called out, banging urgently on the door in front of her, until she saw two people walk around the corner. Quickly realising that she didn't recognise the new arrivals, Elizabeth stepped back, but she soon realised that what she'd done had been enough to attract their attention as they walked up to her door, the man- dressed in a dark blue suit over a light blue shirt, along with a neatly-trimmed beard- taking out a set of keys and opening her door as she retreated to the opposite side of the room.

"Good morning, Doctor Weir," the man said, smiling politely at her. "I'm Doctor Adam Fletcher."

"Where am I?" Elizabeth asked, taking care to keep her distance from the man; maybe her time with John had made her overly paranoid, but she wasn't comfortable with a stranger getting into her personal space like this man was.

"You're in the Acute Care Unit of Willoughby State Hospital," Fletcher replied.

"Willoughby?" Elizabeth repeated, her mind recognising the name even as she looked out of the window to give herself time to confirm her memory. "That's… that's a psychiatric hospital."

"Outside D.C., yes," Fletcher said, smiling at her in that frustratingly encouraging manner that doctors always seemed to use when dealing with patients who'd done something simple after so long being ill.

"I'm on Earth?" Elizabeth said, choosing to ignore Fletcher's slight smile at that statement. "When did I get back?"

"You mean, back to Earth?" Doctor Fletcher repeated, looking apologetically at her. "Doctor Weir, you never left."

Elizabeth didn't know what this man meant by that statement- it could have been anything from a plot to trick her to him simply lacking security clearance to know about the expedition-, but she was starting to feel _very _uncomfortable about this situation…

* * *

As she sat in the doctor's office a few hours later, Elizabeth had no idea how she was meant to feel after everything she'd heard and learned since she woke up.

According to what everyone was telling her, she had collapsed during a treaty negotiation that she hadn't given more than a passing thought to since she'd been appointed the new head of Stargate Command, it was over two years earlier than she thought it was, General Jack O'Neill had no idea what she was talking about when she told him about the Stargate, there was that… _moment_… when General O'Neill's head had done… _something_…

And now, Doctor Fletcher was telling her that everything she'd experienced- everything she remembered of her life since she'd received that fateful phone call from Vice-President Robert Kinsey up to her recent confrontation with the Pegasus Replicators- was nothing more than a delusional breakdown caused by the stress of a treaty negotiation on top of Simon's death in a car accident?

She'd coped with worse than that and she was fine…

But, if they were telling the truth- and so far she had no reason to think otherwise; this was too detailed to be some kind of deception set up by the Genii or something like that, it was too vivid to be a hallucination or dream, and their escape had been too elaborate to be another Asuran trick-, all of her more serious experiences had occurred in an elaborate delusion she'd experienced since her collapse; they hadn't actually happened to _her_.

God… how had her mind come _up _with all that?

"It's actually… rather fascinating, when you think about it," Doctor Fletcher said, looking thoughtfully at her from the other side of his desk, having been studying her file in a thoughtful manner since before she had entered the room. "With your stress already higher than the average due to the particular demands of your job, with peoples' lives sometimes depending on your actions, your mind helped you escape the dual burden of your stress and your grief by creating a world where you could get away from everything associated with their causes, drawing on your old interest in space- you expressed an interest in being an astronaut when you were a child, based on some of the people I've spoken to-"

"People you've spoken to?" Elizabeth repeated, looking sharply at him.

"You came here in a virtually catatonic state; I had to talk with some of your associates to get an idea of your background so that I could help you when you came back to yourself," Doctor Fletcher explained, looking apologetically at her. "I assure you, everything I heard will be treated with strictest confidence; even what we heard you muttering-"

"I muttered?" Elizabeth repeated again, trying to make sense of the story that she was hearing even as she knew that nothing about this situation could ever hope to make sense to her.

"Bits and pieces, anyway; we checked in on you to see if you were making any progress, and managed to pick up some interesting details about your dream," Doctor Fletcher said, pulling out a file and studying his notes. "We weren't aware of the context, of course- all this stuff about the Stargate is completely new, as an example-, but we had managed to piece together that you were dreaming about being in the city of Atlantis, under attack by an enemy force of some sort, and that you were spending time with this… vigilante… who lived in the city?"

"The Phantom?" Elizabeth said, so shocked at this casual revelation of their awareness of her greatest secret that she couldn't even feel bothered to resort to her usually instinctive efforts to lie about her association with John.

She'd actually been… talking about him in her sleep?

"Ah yes, the 'Phantom'," Doctor Fletcher said, looking over his notes for a moment before he turned his attention back to her. "A man whom, according to what we heard, is also known to you as 'John'- a highly generic name, creating the suggestion of it being an alias to limit the possibility that you have actually been told his _real _name and therefore limiting the _true _depth of your connection to him-, and a hero who can handle virtually everything that this new galaxy has to throw at him?"

"Yes..." Elizabeth said, looking uncertainly at the man who claimed to be her doctor, suddenly uncomfortable at hearing John being analysed like that.

"Well, it's simple enough, isn't it?" Doctor Fletcher said, smiling at her in an understanding manner that made her want to punch him. "With your fiancé dead, your mind sought to create a new romantic partner for you; someone who could be just as devoted to you, but who would be simultaneously remain distant from you- I assume that nothing actually… well, _happened_, by the way?"

"No…" Elizabeth said, feeling suddenly embarrassed at the assumption that it was possible for something _to _have happened between her and John in the first place.

The very idea of what Doctor Fletcher had suggested was ridiculous; John was her friend and ally, he wasn't a potential anything...

Was he?

Elizabeth felt almost ashamed to admit it, but now that she thought about it, there _was _something there that she'd always shied away from exploring in depth; even before Phoebus had attempted to use her body to seduce John- something that she never liked to think about for several reasons, the least of which was what she'd felt under his mask; John wore that mask for a reason and it wasn't her place to question him about it if he didn't want to talk-, there had been a part of her that had… thought about it…

But that was only natural; John was an attractive man- even if she had never seen his face, he was physically strong and had a good character; that made up for the fact that he'd always worn a mask, as far as she was concerned- who had done a great deal for Atlantis without ever asking for anything, it would have been strange if she didn't feel _grateful_…

Unfortunately, even if she knew that it didn't actually matter what she thought or felt about a man who didn't actually exist, she couldn't quite bring herself to identify what she _really _felt about him; John defied so many attempts at categorisation that it didn't seem right to try and do it when he wasn't there, even if he….

He never would be…

"Actually, going over some of these notes, the Phantom's presence in Atlantis is one of the most interesting parts of your experience," Doctor Fletcher said, drawing her attention back to the matter at hand as he looked briefly at the file in front of him before turning his gaze back to her. "After all, you're not only living in a legendary city created by an ancient race, but you've formed a connection with a vigilante with a Batman-like reputation who's been protecting that city single-handedly for an unspecified amount of time before you arrived in it."

"So?" Elizabeth asked, looking at Doctor Fletcher in confusion. "It's a bit… outlandish, I know, but what does that have to do with the idea that I… created the Phantom as a substitute?"

"Without meaning to be insulting, why, exactly, would a warrior like the Phantom be interested in spending so much time with a diplomat when there are women like this... Teyla Emmagen on Atlantis as well?" Doctor Fletcher said, looking at her with that pointed stare that doctors always used when they were trying to be comforting while delivering direct news.

"Teyla?" Elizabeth repeated in confusion; she didn't understand what Teyla would have to do with her relationship with John.

"Well, from what we gathered from your dreams, she's basically a native of the culture that has grown up around the idea of Atlantis's creators as… would 'gods' be accurate?" Fletcher asked.

"They… Teyla's people had a lot of respect for Atlantis's creators, but I don't think I'd go so far as to say that…" Elizabeth said, suddenly feeling awkward at Fletcher's analysis of this whole situation.

"Well, the point is, she's from a society that regarded Atlantis as a legend even before the Phantom became a factor, correct?" Fletcher said, allowing Elizabeth to nod awkwardly at him before he continued. "So… if she's a warrior who's been brought up in full awareness of the Phantom's legend, why would he ignore someone who has basically worshipped him in favour of someone who has just shown up in the city and doesn't necessarily share his views on how to deal with his enemies?"

"His goal is the protection of Atlantis; he's not interested in me just to get laid-!" Elizabeth protested automatically.

"But surely, considering the lack of help you can actually give him without 'exposing your connection', it would make more sense for him to contact Teyla if he wanted to offer advice to the expedition, considering how you already trusted her and his own experience allowing him to come up with various explanations for how she came to those conclusions given her… primitive background," Fletcher said, smiling sympathetically at her. "You created this relationship with the Phantom to protect yourself from getting hurt again by creating someone you could be attracted to who would simultaneously never actually be _with _you, because he could never share everything with you."

Elizabeth wanted to protest at the idea, but she was already finding herself lost in thought at the scenario that had just been suggested to her.

As much as she hated to think that she was as messed up as Doctor Fletcher's scenario suggested- how could she do her job if she couldn't even trust her own mind?-, it _did _make sense…

After all, she'd never really understood why John had given her that shield device that she still kept in her jacket pocket; didn't it almost make more _sense _to consider the idea that she'd been hallucinating…?

But she couldn't do it.

Even if Doctor Fletcher provided all the statistics he wanted to confirm that people could live out years in dreams and wake up after only a day or so, what she'd experienced with Atlantis was too _vivid _to be dismissed as a hallucination so quickly, even if she had yet to see anything to suggest that the hospital staff were lying to her.

* * *

Lying in bed that night, her father's pocket-watch on her side table and her medication down the sink- that part might not be appropriate, but she wasn't going to develop drug dependency at a time like this-, Elizabeth tried to rest her practically buzzing mind.

Seeing her mother again had been pleasant, of course- it had been too long since she'd been able to spare time to visit her home-, but that didn't help her escape what she was thinking of; everything she'd been through in Atlantis just felt too _vivid _to be a dream, but at the same time everything she'd experienced here fundamentally made so much more sense.

She wouldn't live in a delusion, but why couldn't she shake the feeling that this wasn't as simple as she was being led to believe?

Looking up, she could only stare at the sight of a shadowy figure, crouched in the ceiling despite the lack of places for him to be standing, some kind of opaque surface between her and the stranger, looking down at her with a sense of what Elizabeth could only describe as protective malice; he was clearly dangerous, but, at the same time, she could tell that he wasn't going to attack _her_.

"John?" she said, the name slipping out without her thinking about it.

She might not be able to see him clearly, but something about the manner of the person above her just made her think of the Phantom, the way she always felt secure in Atlantis just because she _felt _that he was there, the way she knew she could count on him to help when he was needed…

Even if everything she'd seen so far told her he _couldn't _exist, something about that presence just… made her feel safer…

But it didn't make _sense_; John didn't even _exist_, and even if he did, Fletcher had been correct that his 'interest' in her didn't actually fit anything that she knew about him…

Even if John, the Phantom of Atlantis, was somehow real where everything else she'd created in her hallucination was fake, why would he have _ever _wanted to spend time with _her _in particular?

* * *

AN 2: Hope everyone enjoyed that; coming up next, we return to Atlantis, and witness John's own thoughts on Elizabeth's current predicament…

AN 3: I acknowledge that Fletcher may have had too much detail about Atlantis for something he overheard and 'translated' from Elizabeth's mutterings, but I felt it appropriate considering the nanites' objective; they need to undermine Elizabeth's sense of self to take control of her, which here involves undermining her certainty about her relationship with John.


	36. The Phantom in My Mind

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Mystery of the Phantom

Crouching uncomfortably in the maintenance tunnel just off the room that had been designated Atlantis's quarantine facility, John once again cursed his luck.

It could never be simple, could it? No matter what he attempted to do in order to protect this city, Atlantis in particular and the Pegasus Galaxy in general just kept on throwing up a mass of unpleasant surprises, no matter what kind of lengths he went to in order to learn more about the world he'd been unexpectedly dumped in so many years ago.

God… how could he have missed an entire planet of demented nanites-turned-humanoids with a grudge against the human race? He might be limited in his ability to actually search through the database at times, but something that big shouldn't have been _that _easy to erase all record of, no matter how good the Ancients were at their job…

He knew that it was irrational to blame himself for missing something that the Ancients had evidently gone to great lengths to cover up, but he couldn't help it; he had made it his personal mission to protect Doctor Elizabeth Weir, and because of the Asurans he had failed so completely that he was _completely _stuck for how he could help her.

He'd been listening to Doctor Beckett's reports on her condition, so he at least knew what the whole coma thing was about- nanites from that 'Niam' guy had infected her when the Replicator bastard had tried to strangle her in the 'gateship' and were spreading from her brain to the rest of her body-, but that didn't help them in finding a way to stop the damn things. They'd only activated a few hours ago and already they'd spread through her body, convincing her immune system that they weren't a threat as they spread through her system, leaving them with practically free reign to assimilate her body and turn it into a new vessel for their consciousness, unable to kill the nanites biologically or technologically without risking damage to Elizabeth herself…

He knew what had happened to her, but he had no idea how to treat it; he just hadn't _trained _himself for something like this!

Seeing her lying on the bed in that isolation tent, scanners constantly going over her body as the senior staff of Atlantis gathered around her, McKay and Beckett trying to devise some kind of cure while Sumner and Teyla waited for some kind of news on her fate (He'd seen Ronon drop in for a visit earlier, but he'd been all-but-ordered to leave by Sumner on the grounds that he wasn't a senior member of Atlantis's staff even if he was a member of Sumner's team), John had never felt so helpless.

He'd always known what to do to help Elizabeth in the past- get to the right part of Atlantis, advise her on whether or not it was worth visiting a particular planet, show up and shoot whoever was threatening her-, but how could he stop something like this?

God, he couldn't even _talk _to her without risking the rest of the senior staff coming down on him like the proverbial ton of bricks, and after the brutal way he'd treated Lucius he wouldn't blame them; he'd gone _way _too far when dealing with a guy whose only crime was being a smug git, and now they'd seen him as the monster he'd always been trying to ensure he'd never become, which meant that Sumner would probably arrest him the second he showed himself.

He'd give everything he had to save her, but all his strength and skill meant nothing now…

She might be able to hear him, and there was definitely _something _going on inside her head based on Beckett's scans, but that wouldn't do him any good if he wasn't in audible range.

Sometimes, he hated his life…

_Come on, Elizabeth_, he said, staring desperately at her, hoping that thought would suffice when words were hopeless. _Fight these things… don't let them take you from us_…

_Don't let them take you from _me…

* * *

Walking into her house, Elizabeth wished that she could explain why she was so reluctant to accept the world around her.

Even if she wasn't the person she thought she'd been for- as far as she was concerned- the last two years, what did it really matter? She had an interesting and engaging job that challenged her abilities while never pushing her to the point that she couldn't handle the task before her, she had her mother back in her life, she was forming- or should that be _re_forming- a good friendship with General Jack O'Neill…

But, no matter what she tried to do with her life, one thing kept on preventing her from making the last few steps to move on from her delusion.

She might be prepared to move on from Atlantis, but how could she move on from John?

Even if the relationship they'd shared didn't make sense, that just made it all the more meaningful to her, rather than less. Relationships weren't meant to be predictable, no matter how people might like to pretend otherwise; Doctor Fletcher could argue that John was a representation of what she'd been looking to escape after Simon's death, but even if that made sense, Elizabeth still felt that there was more to John's existence than that.

She could understand Fletcher's theory about wanting to remain detached by creating a man who she couldn't commit to because he wouldn't share his identity with her, but surely, if she'd created John to do something like that, he'd have actually shared _something _with her other than professional interaction?

It just didn't quite make sense to her; if John was a product of her imagination to fill the void left by Simon's death, surely they would have actually _done _something together…

Admittedly, now that the idea was in her head, Elizabeth was finding it hard not to think about the possibility of doing something like that, but she wasn't sure how to go about it-

And how the Hell she had allowed herself to get onto _this _train of thought she didn't know; where was the point in thinking about someone who didn't exist? She was already avoiding mentioning the dreams to her mother- the fact that she hadn't told any of her friends or colleagues went without saying-, and had rejected some of the additional medication that Doctor Fletcher had offered as she didn't want to actually _lose _her memories of John…

It made no sense for her to be this focused on retaining the memories of someone who'd never existed, but there was just something about her experiences with John that were more real than anything she'd ever encountered in this world, and she couldn't put that aside that easily.

Where everything else about this world left her feeling emotionally numb at best, just the thought of John left her feeling so alive…

Besides, after Doctor Fletcher and General O'Neill used the _exact _same term to describe her condition, completely independent of each other, she felt that she was entitled to be a _bit _suspicious of the situation surrounding her; she might be drugged, but she wasn't stupid.

If only she could work out what she was missing…

The sudden sense of something nearby her prompted her to turn around, her eyes narrowing as they focused on a nearby door. Walking up to the door, Elizabeth paused for a moment- what if she'd just stumbled across an intruder of some sort?- before opening the door to reveal…

Her eyes widened incredulously.

A _Stargate_…

An _active _Stargate…

Reaching out towards it, Elizabeth could almost _feel _the event horizon…

A hand clapped down on her shoulder, yanking her away from the door before something jabbed into her arm, consciousness rapidly fading from Elizabeth's mind…

* * *

"OK," McKay said, looking around the room at the rest of the Atlantis senior staff, John watching from a small hatch in one wall that gave him a reasonably clear view of Elizabeth and the rest of the room's residents, "we think we've found a way to uncouple the nanite cells from Elizabeth's cells."

"'We'?" Beckett said sceptically.

"How?" Teyla asked, voicing John's own thoughts on the question.

"We create a distraction," McKay explained, holding up a small cylinder marked with a biohazard symbol before Doctor Beckett gingerly took it from the Canadian and put it on a nearby trolley.

"It finally occurred to me why I wasn't having any success…" Beckett began

"What were the nanites originally designed to do?" McKay said, talking over Beckett before the doctor could finish his sentence.

"Fight the Wraith," Ronon said simply.

"Exactly," McKay said with a proud grin. "So that's what we'll get them to do now."

"We think by implanting a small amount of Wraith tissue into Doctor Weir's body…" Beckett began.

"It's like a tumour," McKay said, once again interrupting the doctor.

"Aye, a small tumour, yes," Beckett clarified, assuaging John's initial concerns even if he was still alert for more information about what they were planning to do to Elizabeth. "The nanites will essentially…"

"They'll attack it," McKay explained; for a man who dismissed medicine as voodoo so often, he seemed to take a surprising amount of pride in anticipating Doctor Beckett's medical explanations for the problems they were facing. "They _have_ to- it's what they are programmed to do-, which will draw them away from Elizabeth's cells, effectively unbinding them."

"It will only last a few seconds or so, mind you, before the nanites attack the Wraith tissue and return their focus to Doctor Weir's cells," Beckett added.

"Yeah," McKay said, acknowledging the odds with a brief concessionary nod at Doctor Beckett, "but that's all we need: momentary distraction to draw them away from her so we can zap 'em with the EM pulse."

"Very well," Sumner said, in that grim tone of his that John had never liked; it sounded far too much to him like Caldwell wasn't really that concerned about the potential risks of what he was doing, so long as there was a chance of success.

This was Elizabeth's _life_, and Caldwell was just treating it like another goddamn day at the office when they were planning to inject her with Wraith DNA…

He had as much faith in McKay and Beckett's skills as he could have without having actually worked with them directly on a long-term basis, but when it came to Elizabeth, he was certain that he would have been anxious regardless of who was responsible for this procedure and what they were attempting to accomplish with it.

* * *

As soon as she woke up in the hospital room where this whole experience had started, Elizabeth was already working on planning her next move.

Regardless of what had happened to her before her apparent 'breakdown', she had been making good progress with her recovery- particularly with her disinclination towards certain drugs, even if she hadn't been totally honest about her reasons for not taking them-; there was _no _reason for hospital orderlies to have just… _shown up_ like that.

She might have been prepared to let it go in the past, but if her time with John had taught her anything, it was the importance of trusting her instincts in any situation, and right now the mess that she was in was too confusing for it to be reality.

"Hey," General O'Neill's voice said, prompting her to turn and look at him as he leant against her window ledge, looking at her in an unusually solemn manner for the usually jocular general. "How're you feelin'?"

"Why am I back here?" Elizabeth asked, testing the waters with the most obvious question.

"They're worried," Jack said. "Frankly, so am I-"

"So worried that they showed up in my _house _while I was 'hallucinating'?" Elizabeth interjected, glaring at Jack in frustration. "What is normal about that?"

"The doctors just want to make sure-" Jack began.

Elizabeth didn't even want to hear it any more; she had no idea where she was or what was happening to her, but there was no way that she was unstable enough for hospital orderlies to have been monitoring her as closely as that.

Which meant that this scenario didn't make sense.

Which meant that this world she was in _wasn't _real.

"You disappoint me, Elizabeth," Doctor Fletcher said, walking into the room with a pitying look on his face. "I thought you wanted to get better-"

"I _am _better," Elizabeth said, looking firmly at the man she was increasingly convinced wasn't even here. "I don't know what happened to leave me here, but I do know that this is _not _reality-"

"Elizabeth," Doctor Fletcher said, with an obviously false sense of regret in his voice, "I'm sorry, but you don't leave me any other choice…"

* * *

"Oh no…" Beckett said, as he studied the displays on the screen before them.

He'd been _so _sure that he'd had the solution with the EMP attack, and now there were _still _nanites accumulating at Elizabeth's brain…

"We didn't get them all," he said, looking grimly back at the other senior staff.

"How is that possible?" Teyla asked.

"I don't bloody know," Beckett said, his tone grim as he moved away from his position at the scanner to walk over to where McKay stood alongside the EM-generator.

"They've been using organic material to replicate, which has rendered them immune to the EM pulse…" McKay said, looking grimly at the read-outs on the screens next to him.

"So… now what?" Ronon asked.

"They've started replicating again," Beckett said, studying the screens as though praying that some kind of solution would jump out at him.

"What do we do now?" Teyla asked, even as the display screen showed the remaining nanites moving into other parts of Elizabeth's brain.

"I don't know," Beckett said, looking grimly at the city's leader as she lay before him, urgently requiring help that he couldn't give her. "We can't use the EMP again; most of the nanites have migrated into the arteries that supply blood flow to the higher functions of her brain…"

"_No_," a voice suddenly said.

Spinning around, the senior staff were shocked to find the Phantom standing in the corner of the infirmary, creating his usual formidable impression in his long black cloak as he glared at the group before him.

"Elizabeth Weir does _not _die like this," he said firmly.

"Uh… excuse me?" McKay said, overlooking his shock at the Phantom's arrival in favour of focusing on what he could control. "I don't know if you've been paying attention- although, considering your timing, I'm guessing that you have-, but we're out of options-"

"Because you've not been paying attention," the Phantom said, looking over at the Canadian. "You haven't even considered the implications of Doctor Weir's mind still showing activity in this condition."

"What are you talking about?" Beckett asked, putting his shock aside to look at the Phantom.

"What will the long-term consequences be for Elizabeth if the nanites take action in their current position?" the masked man asked.

"Well…" Beckett said, confused at the other man's line of reasoning, "reducing blood flow to those parts of her brain will put her into a state of cerebral hypoxia…"

"Exactly," the Phantom said.

"Excuse me?" McKay said, looking at the masked man as though he'd lost his mind. "Carson just told you that they're going to _kill _her-"

"They'll render her _brain-dead_, Doctor McKay, which fits the pattern of computers trying to erase an old program and work on a new one; shut down the previous hard-drive so that you can add your own program to it that overrides the pre-existing one," the Phantom corrected, a slight smile on his face as he made his announcement. "You're dealing with Replicators, Doctor; they see the human body as nothing more than another machine, so when these nanites infected Doctor Weir, they probably concluded that the best way they could get anywhere was to take control of the 'machine'."

"You mean… they've been trying to replace Elizabeth's consciousness?" Doctor Beckett said, looking at the masked man in new in understanding.

"And her mental activity reflects the conflict as the nanites try to enforce their programming on her while competing against her own mental efforts to resist them," the Phantom finished, a slight smile on his face as he nodded in confirmation at the other man's theory.

"A battle of wills," Teyla said, looking reflectively at Elizabeth.

"This is all a fascinating theory, but it's still only that," Colonel Sumner said, looking at the Phantom with his usual penetrating stare.

"Her neural activity does support… the hypothesis, Colonel Sumner," Doctor Beckett said, looking over at the colonel with a slight smile. "And besides, it certainly fits better than any other theories I've been able to come up with for what these things are trying to accomplish; we aren't exactly dealing with mindless automatons, you know…"

"Exactly," the Phantom said, smiling grimly at the staff around him. "We may be dealing with a bunch of deranged nanites, but they're still Ancient technology, which means that not only are they very smart, but also means that I'm _uniquely _qualified to deal with this particular mess."

"What-?" McKay began, before the masked man turned around and walked into the quarantine sheet set up around Elizabeth.

"_Don't_-!" Beckett yelled, only for his words to fall on deaf ears as the mysterious guardian of Atlantis placed his hands on Elizabeth's arm…

* * *

As a new wave of orderlies entered her room, clearly intending to take her somewhere else, Elizabeth quickly chose the only option left to her; she drew back her fist and punched the approaching man with everything she had, unable to resist a sense of satisfaction as she felt his nose give under her fist.

Natural diplomacy forgotten in the face of the current threat, Elizabeth, her mind racing as she recalled everything she'd picked up from watching the occasional training session or encounter with John- as well as whatever was left over from Phoebus's time in control of her body-, lashed out at the orderlies around her, knocking them down long enough for her to the run to the door of her room. Doctor Fletcher moved to try and catch her, but a violent shove forced him out of her way before she began to run down the corridor, scanning the walls for some clue about where she could go next before she dived impulsively into an elevator and hit the button for the lowest level; she could work out where to go once she was out of the hospital…

The sight of the corridors of Stargate Command when the elevator doors opened might have confirmed that she wasn't dealing with reality, but it only provided a certain amount of comfort and reassurance; knowing where she wasn't didn't help her work out where she _was_.

"Elizabeth…" a voice said from down the corridor, Elizabeth turning in the direction of the voice in time to see the man she'd been told was only in her head.

"_John_?" she said, looking at her city's vigilante guardian incredulously, the Phantom standing in the middle of the corridor that she only now registered led to the gateroom with a firm stance that made it clear he wasn't going anywhere.

She'd accepted that this wasn't real, but to see such definitive proof that _he _was real…

"What's going on?" she asked, looking at him in desperation, praying that he could provide her with answers the way he always had in the past.

"You've been infected by nanites," John replied,

"They're trying to take control of your mind and body."

"What do I do?" she asked, relieved to have some kind of other explanation for what was happening to her; she might not understand quite how the nanites could have infected her, but after some of the things she'd read about in the SGC mission reports, it wasn't impossible to assume that they were somehow manipulating her brain's perceptions…

"Fight this, Elizabeth," John said, staring firmly back at her, his long black cloak and silver mask a bizarre sense of normality in a world that had seemed so strange because it was _too _normal. "You have to come back to me…"

The pain in the last word as he looked at her, as though the idea of her not coming back was the most devastating thing that could ever happen, was enough to convince Elizabeth that she was dealing with reality.

"What do I do?" she asked him.

"Go to the gateroom," John said, still staring at her in that same intense manner that only he could achieve. "Come back to Atlantis… come back to _me_…"

John began to fade away even as he spoke, but Elizabeth wasn't going to worry about that; she had further proof that this wasn't real, and that was all she needed right now. Focusing on his instructions, Elizabeth ran along the corridor, the presence of two soldiers in her path with guns in their hands barely registering to her as she ran through them, her attention focused on her final goal of getting out of this place…

Finally, she came to the gateroom, and ran up to the control room, her brief time in charge of the SGC enough for her to remember how to activate the console and dial the address she needed. Looking up, she smiled at the sight of the Stargate with an active wormhole within it, all seven standard chevrons illuminated in the 'locked' position, along with the faint glow of an eighth chevron underneath the ramp leading up to the wormhole. With that done, Elizabeth ran from the control room down to the gateroom, hurrying up the ramp leading to the active wormhole, only to come to a halt as a familiar figure stepped in front of her.

"I can't let you go," O'Neill said.

"You're not General O'Neill," Elizabeth said, glaring at the man before her, her gaze not faltering even as he transformed into Doctor Fletcher; it was almost refreshing to see that whatever was behind this was willing to abandon the lies now.

"Elizabeth, listen to me-" he began.

"You see that?" Elizabeth said, pointing at the Stargate behind him. "That's the Stargate, and yes, leaving is _exactly_ what I plan to do."

"I won't let you go," Doctor Fletcher said once more.

With no other options left to her, and whatever good humour or diplomacy she might have had exhausted by her frustration at this whole situation, Elizabeth struck Doctor Fletcher in the face, sending him flying to the side of the platform. With the only immediate obstacle in her path removed, Elizabeth took a deep breath and walked through the Stargate…

* * *

When she opened her eyes once again, Elizabeth found herself lying on a bed in the quarantine facility, looking up to see Colonel Sumner and Doctor Beckett getting up from the ground, while McKay leant against a wall in a dazed manner and Teyla and Ronon looked slightly awkwardly at each other.

"Hello," she said, looking at them uncertainly. "Uh… what just happened?"

"Well, you were being used by a bunch of Niam's nanites, then the Phantom dropped in and touched you before bailing out on us…" McKay said, looking momentarily daze before he shook his head as though trying to clear it and turned to face the nearest wall. "And just so you know, if you end up spreading those nanites because you didn't want to get checked out, I am going to make _sure _we shoot you in the head that you _clearly _don't use-!"

"Rodney?" Carson said, looking at the scientist with a slightly frustrated stare. "Can you please stop talking to the man who's probably fully aware of what he might have done to himself- and, if past precedent is anything to go by, probably already has some idea of what to do about it-, and help me make sure that Elizabeth is all right?"

Looking at the wall that Doctor McKay had been addressing- most likely it contained one of those secret passages that John was always not-so-subtly hinting he was aware of throughout Atlantis-, Elizabeth allowed herself a brief smile at the thought.

She was back in Atlantis, John was real, and he'd just proven himself to her once again…

Her smile faltered as another thought occurred to her.

Doctor Fletcher might have been a nanite-induced hallucination, but one thing he'd said had stayed with her; why was John particularly interested in _her_ of all people…


	37. To Him, I Am Beauty Beyond Compare

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Jumped forward a bit; this chapter's set while McKay's back on Earth for 'McKay and Mrs Miller' (Let's just say I have plans for 'Common Ground' that necessitated it being skipped on this occasion, even without the fact that Sumner would be less open to the idea of an alliance with Todd…)

Mystery of the Phantom

Standing on her balcony, Elizabeth wondered why she should expect this particular attempt at a meeting to work out any better than her other recent efforts.

Ever since she had woken up from her nanite-induced coma, she had spent two or three 'sessions', each a few minutes long, out on 'their' balcony each day, waiting for some sign that John would come back to see her, but he'd been maintaining the distance that seemed to have settled over them since that whole mess with Lucius.

Was this how it was going to be between them now? John remaining distant because he felt… something… about that time that he hadn't shared with anyone else, only showing up when they needed help, and otherwise ignoring her attempts to reach out to him?

It wasn't that she didn't respect John's wishes; she just wished that she could understand what had driven him to make that kind of decision. She had initially wondered if it was something that she'd said under Lucius's influence, but dismissed that idea almost as soon as it had occurred to her- John had to know that she didn't really feel that he couldn't be trusted because he wore a mask, right?-, and she was left wondering if the explanation lay in something else.

"Is all well?" a voice asked, ending Elizabeth's thoughts as she turned to look in relief at their subject.

"John," she said, smiling at him in relief. "You're all right?"

"You mean the nanites?" John said with a smile. "I'm fine, thanks; I think that the nanites were both too focused on you to spread to me and I had too much control to let them access me."

"Control?" Elizabeth repeated in surprise. "You could _control _them?"

"They were Ancient technology, Elizabeth; they may not have been designed to respond to ATA-gene control, but that's only an obstacle rather than a handicap to someone as experienced with the stuff as I am," John explained with a smile. "I was able to make a degree of contact with you by remote, but you only experienced me as me when I made physical contact and completed the circuit; you were already fighting their attempts to reprogram you, but I just… gave you something to focus on."

"That was you?" Elizabeth said, recalling the impression she'd sometimes received that something was watching her in the illusion. For a moment, she thought about hugging John, but considering what he must have been through here she decided against it- she'd met too many battle-trained soldiers who had spent so long in the field that they reacted to every moment of physical contact like it was an attack-, settling for smiling warmly at him. "Thank you."

"You're welcome," John said, before he looked at her with his more traditional neutral expression. "So, is this current meeting about Doctor McKay's latest experiment?"

Elizabeth tried not to let her disappointment show at his last comment; had he only come here to discuss their latest potential danger?

It might be weird to think about something like that when so much was riding on the knowledge that they could acquire from Atlantis, but the fact that he'd come here just because of what they were about to do…

"Well… partly," she said, looking at him uncomfortably. "I mean, if you have any input to offer, we'd appreciate it, of course, but really, I just… ever since that whole thing the Replicators and Niam's nanites, I've needed to talk about it, and…"

"And you haven't found anyone to talk to here?" John asked, looking at her in confusion. "You have a trained counsellor on staff-"

"Who's obliged to report back to Earth with her results; I just…" Elizabeth began, before she sighed in uncertain resignation as she looked at him. "With the way things have been recently, I just feel like… some people are _waiting _for an excuse to get me out of the city…"

"And you're not going to give them that excuse, huh?" John asked, with a slight smile on his face as he looked at her; only a slight tension in his fists hinted at the part of himself he had shown so often in defence of this city. "And you think I'm a good alternative?"

"Whatever else you are, I know I can trust you," Elizabeth said, looking firmly at him, already psychologically committing herself to take advantage of the opportunity to unburden herself in face of the one person she always felt inexplicably safe around, despite the mysteries surrounding him.

"All right," John said, looking at her with a warm, soft smile. "What do you want to talk about?"

For a few moments, Elizabeth simply stood and stared out at the ocean before her, all thoughts of what she would say to John when they next spoke suddenly inadequate when faced with the chance to actually say them, until she finally found something to say that didn't feel quite as awkward as the alternatives.

"I still can't quite get over it," she said at last, stuck for a better way to start the ball rolling. "We find a surviving Ancient colony, and it's populated by machines that are perfectly willing to destroy us because they resent the fact that the Ancients chose us over them, stop the destruction of Atlantis by the skin of our teeth…"

"Let's just take it as a win right now," John said, smiling reassuringly at her. "After all, from what I heard, you kicked those nanites' asses when you got the chance…"

"Which I only had thanks to you," Elizabeth said, smiling over at him. "I know I was only in there for a few hours, but…"

"Felt like longer?" John asked, looking at her with a slight sense of anxiety.

"A lifetime," Elizabeth admitted, lowering her head for a moment before she looked back at him with a smile. "And I never would have managed to escape it without you."

"Eh, I didn't do that much; Doctor Beckett dealt with the worst of them-" John said with an awkward smile; it was as though discussing what he'd done was a lot easier than thinking about how it made her feel.

"But _you _worked out what they were doing to me," Elizabeth said, looking at him with a reassuring smile, slightly amused at his apparent discomfort

"Hey, that was just a theory that turned out to be right; don't praise me for being lucky," John said, the smile faltering slightly as he looked at her. "I would have tried to help out earlier, but it was only really a theory until Doctor Beckett confirmed what the nanites were doing and how your body was responding to it…"

"You saved me in the end; that's what counts," Elizabeth said, smiling reassuringly at him, before her expression became more pensive.

She couldn't believe that she was feeling awkward about this; she'd negotiated treaties that could have resulted in war if something had gone wrong, and she was _still _awkward when asking a guy a personal question?

Then again, it wasn't like this was _any _guy… she was talking to the _Phantom of Atlantis_…

"It's just…" she said, briefly wondering if it wouldn't be easier to just not bring this particular topic up in the first place before she took a deep breath and metaphorically dived in to the real question. "Why me?"

"Pardon?" John asked, looking at her in confusion.

"Why do you… spend time with me?" Elizabeth asked, looking uncertainly at him; now that she was actually talking about it, her confusion seemed slightly pathetic, but she'd made her choice and would have to go along with it. "I mean, Teyla seems like she's… more your type, when you get down to it; she's the warrior who's been raised on your legend, she'd believe you if you went to her for help, I would have listened to any suggestions she had to make even if she had revealed that they came from you…"

"Hold it right there," John said, looking at her with a slight smile that she couldn't quite place the nature of. "Yeah, Teyla's a warrior who knows details of my history, and she's… well, I'll concede that she's not bad on the eyes…"

"But?" Elizabeth asked, ignoring the stab of what had almost felt like- but was definitely _not_-jealousy that she had felt at the reference to Teyla's… physical attributes; this wasn't high school and she _wasn't _the book-club girl jealous of the head cheerleader…

"But," John said, looking at her with a warmth that she rarely saw him express, reaching over to place a comforting hand on her arm, "in the two decades I've been in this galaxy, doing my duty to protect the Wraith, you gave me something I've never had before."

"I… I have?" Elizabeth said, uncertain if she should feel unnerved or flattered at the implications of John's statement; she'd only been here for a couple of years, and had spent so comparatively little time with him during that time, she didn't really get how she could have had that kind of impact on someone who'd been her for ten times that…

"You gave me a _purpose_, Elizabeth," John said, looking at her with a warmth that she couldn't recall anyone ever directing at her before, a tenderness about John that she had previously never thought to associate with the Phantom. "I spent years stopping Wraith from feeding because I didn't like them… but you gave me someone to do it _for_."

There wasn't really anything that Elizabeth could say to that statement; she just stood and stared at John for a few moments, moved by his words while lost for how to respond to them, barely even registering the anomaly of her being lost for the words that were usually the way she made a living…

A sudden shift in John's manner was the only clue she had about what he was about to do before he jumped over the balcony in his usual more extravagant manner of departure, leaving Elizabeth looking awkwardly after him.

What had he just admitted to?

Why was he so apparently reluctant to tell her any more about the reasons for his interest in her?

Could he…

_No_.

That would have been…

It was just Doctor Fletcher's words making her think too much about it; she _wasn't _interested in John that way…

But how much of that was because she thought he couldn't be interested in her?

No matter what John had said about her giving him purpose, she didn't understand _how _she'd done something like that…

* * *

AN: Now my longest, but I can assure you that Elizabeth will encounter a _much _more significant clue in the next chapter…


	38. Same First Name

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Another jump forward, this one exploring Rod's time on Atlantis in 'McKay and Mrs Millar'; all details of our McKay's reunion with his sister and her trip to Atlantis so far are pretty much the same as they were, minus Sheppard slightly flirting with her for obvious reasons

Mystery of the Phantom

Among all of the unusual experiences she'd had since coming to Atlantis, witnessing Doctor Rodney McKay interacting with a man who both was and wasn't him had to be one of the weirdest.

It was actually rather interesting to see how McKay could have turned out under other circumstances, of course- Rod was clearly still as intelligent as McKay, but he just had a different manner of interacting with the rest of the expedition-, but the rest of Elizabeth was wondering how they'd cope with Rod in the long term. Putting aside her vague recollections of some kind of side-effect caused if two versions of the same person were in the same universe as each other for too long- it had been a long time since she'd read that report and she'd never expected this kind of situation anyway-, she wasn't sure how McKay would feel about giving orders to himself, even if Rod seemed like he'd be perfectly comfortable not being the superior in the situation.

Actually, she had to admit that Rod appeared to be far more comfortable working with them then she would have expected. He'd been rather surprised to see Sumner when he'd arrived- apparently Sumner had been killed by the Wraith during their first encounter with them in Rod's timeline-, but Sumner had dismissed it as an irrelevant item of news and was focusing more on questioning Rod about his past in case his history included something that they hadn't encountered yet.

"So… you're on the Athosian High Council in your world?" Sumner said, looking at him curiously as he, Rod and Elizabeth sat in her office discussing his world. "How did that happen?"

"Helped them reclaim their homeworld after the initial Wraith attack a year or two back; things just… fell into place from there," Rod said with a smile, before something seemed to occur to him, the other scientist looking curiously at the gateroom outside the window for a moment before he looked over at Elizabeth and Sumner. "That reminds me; where's Colonel Sheppard?"

"Colonel who?" Sumner asked.

"Colonel John Sheppard," Rod clarified, looking at Sumner in surprise. "You know, genius military officer who makes this me look humble, possesses an Ancient gene so powerful that he makes everyone else look like they're just trying to play the piano while he's completing Scherbert's last symphony?"

"I… don't think we have a Colonel Sheppard," Elizabeth said, looking at Rod in confusion.

"Uh… _Major _Sheppard ringing any bells?" Rod asked, looking over at Sumner. "I mean, if you're still alive, maybe he never got promoted to that level…"

"We have no John Sheppard affiliated with the expedition to the best of my knowledge, regardless of his rank or the level of his ability to control Ancient technology," Sumner said, looking firmly at Rod. "Is there a particular reason you're bringing him up?"

"Just… surprised he's not here, that's all; guy might have had an ego that would make your me look humble, but he earned it," Rod said, shrugging awkwardly at Sumner's stare in his direction. "Member of my Atlantis's chapter of MENSA, leader of Atlantis's military, natural understanding of most Ancient technology…"

As Rod continued to speak, Elizabeth's mind started to drift as she contemplated what she'd just been told.

Could it be?

John wasn't exactly an uncommon name, and it could be that he'd just chosen that name because he'd heard enough of the expedition talking about Earth to know that it was a common one…

But, on the other hand, if Rod's reality had most of the same personnel with the addition of a lieutenant colonel with that name and skill with Ancient technology, was it possible that the reason for his absence from this reality and the Phantom's presence on the city were the same?

She'd probably only be able to look into that when she was back on Earth for her next debriefing, but it was something to consider…

* * *

_Shit_, John thought to himself from his position in the maintenance tunnel off the commissary, noting the contemplative expression on Elizabeth's face after Rod's latest question.

It might not be particularly meaningful to anyone else- they'd assume that she was just curious about this person who would have been part of the expedition in another lifetime-, but he knew that Elizabeth was already putting together the pieces of a puzzle that nobody else even knew about.

Of all the ways he'd imagined Elizabeth somehow learning his surname, the idea that she'd hear it from someone from an alternate reality where he was an official member of her staff had never been one of them…

OK, in a weird way, it was comforting to hear that he may have come to Atlantis even if he'd had a normal life, but considering how he'd apparently turned out in that reality, he felt like his arrival under these circumstances had been for the best; his other self sounded like a dick at best.

If that was what he would have become if he hadn't come to Atlantis, he was glad that he'd come here; everything he'd endured was worth it if he was someone people could respect, rather than someone so goddamn self-assured he made _McKay _look humble.

In the end, however, the fact remained that Elizabeth wasn't stupid; with the information that she'd heard today, coupled with everything else she'd learned about him over the past year, it wouldn't take her too long to work out who he really was.

He just… he wasn't _ready_…

Why couldn't the universe cut him a break?

* * *

AN 2: Short, but we're approaching the big moment; next chapter goes to "The Return"…


	39. What's in a Name?

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: As promised, we've gone straight to the events of "The Return"- nothing really changed much for the rest of Rod's time in Atlantis or during the events of "Phantoms", so I didn't bother rewriting them-, shortly after the expedition has been 'asked' to leave the city…

Mystery of the Phantom

Standing on her balcony for what may be the last time, Elizabeth almost couldn't believe it.

They were being _kicked out_?

She'd spent three years working with the members of this expedition, and now they were being ordered to pack up and go their separate ways just because someone else objected to their presence in Atlantis?

All right, so the Ancients were the original builders of Atlantis who'd just been recovered from centuries trapped in a weird form of diluted time perception that Elizabeth didn't fully understand, but after all the time they'd spent in the city, to be told that they should just get out even when the Ancients were only there because of their efforts…

She'd done everything she could, and it still wasn't good enough for them; the Ancients were acting as though they were still nothing more than ignorant savages who'd moved in to an ancient city and messed up the system. They might have made some mistakes, but they were still leaning everything they could about Atlantis, and some of those mistakes had been the result of the Ancients themselves not leaving clear instructions; it wasn't their fault that the Ancients had been too arrogant to make notes about how they'd failed…

Admittedly, they were still in control of the _Orion_, but that was mainly because it was back in the Milky Way galaxy at the moment undergoing some additional repairs- the SGC had expressed some hope that they'd be able to use the Antarctica research site to find ways to improve _Orion_'s own drone reserves- and everyone concerned had agreed to keep quiet about it. Considering that ships were easier to manufacture than Atlantis, Elizabeth doubted that the Ancients would be as concerned about reclaiming _Orion _as well, particularly in its current damaged condition, but it was easier to retain a hold of it when it wasn't on Atlantis. All records of _Orion_'s presence in Atlantis had been kept primarily on the expedition's own hard drives rather than Atlantis's own computers, and those were all going back to Earth with them, so by the time the Ancients found out about the ship, the SGC could probably claim that they'd recovered it as salvage in the Milky Way and leave it at that.

"I'm sorry," John's voice said from behind her.

"For what?" Elizabeth asked, smiling weakly at John as she turned around to look at him; she might resent the fact that she was losing Atlantis, but she'd never resent John for anything.

"That I can't do anything to keep you here," John said, looking sadly at her. "I can't exactly drive the Ancients out of Atlantis without compromising any possibility of an alliance with them, and I think we're both aware by now that I don't have any real influence over the Ancients themselves…"

"It's all right," Elizabeth said, smiling briefly at him; she still hadn't found the time to actually talk to him about Rod revealing his real name, but the fact that he was willing to even acknowledge that he wasn't an actual Ancient…

"I can't come with you."

"_What_?" Elizabeth said, looking at the masked man incredulously, her earlier thoughts pushed aside with this sudden admission. "You're staying _here_? But the Ancients-"

"They're never going to find me- Atlantis has been programmed not to register my lifesigns unless I want it to register that I'm there, and the Ancients are never going to be able to find that program unless I tell them where to look-, and I don't… well, I think we all know I don't belong on Earth," John said, shrugging slightly awkwardly as he looked at Elizabeth. "I'd like to think that I've been a lot of help to you over the last year or so, but we all know that Sumner's never going to accept me as an official part of the team. Even if his superiors did, there's only a few commanders back at Stargate Command I'd respect enough to take orders from, and I somehow doubt that they'll assign someone like me to a position where I'd be reporting to anyone on that list..."

"Easier for who?" Elizabeth asked, glaring at him.

"Wh- Elizabeth, we both know that the SGC isn't going to just welcome me to Earth-" John began.

"You're not even going to _try_," Elizabeth said, staring coldly at John, trying not to analyse just why she felt so strongly about his decision. "You've gone through so much for us, and you're just going to _leave_-"

"We both know that I'm still considered a rogue element back on Earth, Elizabeth," John said, his expression grim as he looked at her. "I know that there are some people who'd try to do the right thing for me as an individual, but with my knowledge of Ancient tech they'd be overwhelmed by the people who'd consider me an asset and nothing more; it's easier for everyone if I just stay here-"

"John Sheppard, don't you dare!" Elizabeth yelled, the words bursting from her before she could stop herself as he turned towards the edge of the balcony.

As soon as the words had passed her lips, Elizabeth wished that she could take them back- this wasn't the kind of situation where bringing up his name would be remotely comfortable for anyone-, but when John froze mid-motion, Elizabeth knew that she had no choice but to follow up on the topic she'd just introduced.

"That's your name, isn't it?" she said, looking at him, keeping her voice at a slow tone so that John wouldn't be provoked into leaving before she'd said her piece. "Your name's John Sheppard… and you were born on Earth."

For a moment, silence dominated the balcony, Elizabeth staring at John while John stood on the edge, each one waiting for the other to give in first, until John finally broke the silence with a sigh.

"It doesn't matter," he said at last, looking back at her.

"What are you talking about; of _course _it matters!" Elizabeth protested; she might not have meant to bring this up, but she wasn't going to ignore it now that it was out there, particularly when John had virtually confirmed her theory by his lack of denial. "You're _from _Earth, John; we can take you home-!"

"John Sheppard died over twenty years ago, Elizabeth," John said, turning around to look at her grimly. "There's only the Phantom now… and there is nothing that Earth has to offer right now that the Phantom would want."

As he looked back at her for a moment, Elizabeth had the sudden feeling that John was trying to tell her something, but she had no opportunity to analyse that feeling further before John turned and leapt off the balcony, vanishing into the depths of the city before she could think of anything else she could attempt to stop him.

"Great…" she said out loud, staring up at the sky that she would soon never see again.

Her last chance to get some personal answers from her city's mysterious guardian, and he'd gone and vanished on her, leaving her with nothing more than an ambiguous confirmation of his true name.

The only good thing about her going back to Earth now was that she'd have the chance to do some actual research on whoever John Sheppard had been before he became… what he was now; maybe if she could work out how the Phantom had actually ended up in Atlantis in the first place…

AN 2: Next up, we're back on Earth, as Elizabeth learns exactly who she's dealing with…


	40. The Phantom Speaks

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Alternating between Earth, as Elizabeth carried out her research into her former city's masked protector, and Atlantis, as the aforementioned protector has a 'chat' with its new residents…

Mystery of the Phantom

Sitting in her apartment, Elizabeth sighed as she finished typing up her latest sentence, once again feeling the pointlessness of everything.

She'd been trying to distract herself from the pointlessness of her life by looking over a few new treaties for the President, but she'd been unable to really concentrate on anything that didn't relate to the SGC or Atlantis- which she was still being ordered to remain away from-, leaving her stuck for any immediate activity…

It was strange; Atlantis took up so much of her time that she wasn't sure she'd done anything for leisurely purposes for years- discounting her meetings with John, which were mostly for work purposes more often than not-, but now that she had that time to relax, all she wanted was to get back to work.

She might have been a diplomat rather than a governor, but she'd grown so used to working in Atlantis that it felt wrong to be back on Earth; no matter what job she was offered, nothing could match the satisfaction she'd felt when she was in command of Atlantis, and even treaty negotiations seemed so small after negotiating alliances with other worlds against an enemy that would devour them all if given the chance…

She barely even had any kind of life right now outside of her half-hearted attempt at writing a set of memoirs that would have been classified beyond most levels that she could conceive of if she'd tried to get them published. She'd had relatively few friends before going to Atlantis considering the demands of her job, and of those she'd made in the city itself, Teyla and Ronon had remained in Pegasus, Carson and Rodney were busy with their new jobs at the SGC and Area 51 respectively, and Sumner…

Well, she knew that he was working at the SGC, but they'd barely had anything more than a professional relationship back on Atlantis, and he seemed perfectly content to leave it at that now that they no longer worked in the same city; she didn't actually mind one way or the other, but it felt slightly insulting to realise that someone she'd spent over two years working in close proximity to had no real interest in continuing the discussion.

Finally, with nothing else to keep her occupied but repetitive trains of thought, Elizabeth turned her attention to focus on the question that had dominated so much of her spare time in Atlantis; the true identity of the Phantom.

It had been a strange way to find a clue, but Rod's unintentionally-provided information had helped her crack the most obvious problem in that search. John Sheppard still wasn't an uncommon name, but focusing on John Sheppards old enough to match the Phantom's physical capabilities, coupled with any records of those John Sheppards mysteriously disappearing, had allowed her to narrow down the suspect list significantly.

After a few more hours of independent research, she felt that she had finally identified the John Sheppard she was looking for. With other candidates dismissed on the grounds of age, a continued presence on Earth- she wasn't going to consider time travel until she was sure all other options were exhausted-, and other factors allowing her to discount the other possible John Sheppards, her search had finally led her to various newspaper articles about the disappearance of John Sheppard, the fifteen-year-old son of utilities mogul Patrick Sheppard, over two decades ago during a family holiday in Britain.

From what the article revealed, Patrick and John had argued during their first week on vacation in Glastonbury and John had left the hotel in a huff, claiming that he was going for a walk in the area. His mother had reported seeing him enter the woods near their hotel after the fight- she'd thought that it was best to give him time to cool off on his own, and the hotel was fairly easy to find your way back to-, but he had subsequently dropped off the metaphorical map and never been seen again; his father had tried to arrange various searches in that area after John had been missing for a day, with search efforts expanding as time went on, but interest in the case had eventually died down after a few months with no breakthroughs and no sign that anyone would be stepping forward to claim responsibility.

According to some of the information they'd revealed in subsequent interviews, John had been interested in joining the Air Force as a child, which added further weight to the idea that he was the Phantom. An interest in the Air Force would give John the right psychology to become the Phantom- his mother had stated in her interviews that John was always interested in protecting others when speculating why he might have gone missing, which translated into an obvious 'hero complex'-, particularly with the skills he'd demonstrated in using the gateships during those occasions when he'd taken one from Atlantis's various hangers…

The discovery at least explained where John had come from, and the holiday taking place in England suggested some possibilities- considering what the SGC had recently learned about Merlin being an Ancient, it was possible that John had stumbled across some kind of Ancient teleportation device that had sent him to Atlantis-, but that still left her with more than a few questions.

For one thing, how had John learned anything about how to operate Atlantis? He wasn't stupid, but nothing she'd read about John Sheppard's past indicated a strong interest in ancient languages; he should have been incapable of even reading the city's operating instructions, never mind everything else he'd learned from the city's archives over the years.

On top of that, other questions included why he hadn't just decided to return to Earth once he'd discovered its address in the database, why he had decided to start going around in a mask and cloak rather than a less theatrical outfit… why he was so interested in her…

No matter what other theoretical explanations she came up with for what had happened to John, none of them accounted for his continually-expressed interest in her; what was it about her that inspired that kind of interest?

His explanation had sounded good at the time she asked him that question, but it didn't help her understand the obvious depth of his interest in her; even if he was from Earth, what had prompted him to try and talk to her, risking his safety by 'targeting' someone at the top rather than making contact with someone lower in the expedition's command structure and less likely to attract attention…

Even when she was fairly sure she knew who he was, all she found herself with was more and more questions; what was it about the Phantom that made everything so complicated?

She just… she almost didn't _want _to think about that particular issue; thinking about the Phantom… _like that_… made things feel more difficult than she was prepared to admit…

* * *

Crouched in the maintenance tunnel outside Elizabeth's office- and it _was _Elizabeth's office; the fact that someone else was using it right now was just a temporary inconvenience that John was certain would be resolved eventually-, John felt like growling in rage as he saw Commander Helia sitting casually behind the desk that should belong to the woman who had given so much to preserve this city.

He'd stood by for a few weeks to give her and her crew the chance to come to their own conclusions and do the right thing, but so far their only concession had been to allow General O'Neill and Richard Woolsey to remain in the city as Tau'ri 'observers', and what he was seeing gave no impression that they were interested in doing anything for the rest of Pegasus; they weren't even expressing the slightest interest in helping anyone cope with the Wraith's presence despite the fact that the Wraith were only even there because the Ancients had been screwing with things that shouldn't be messed with…

With General O'Neill and Mr Woolsey in another part of the city at the moment, and the rest of the Ancients working on making Atlantis habitable on a larger scale- they seemed to prefer to spread out where the expedition had concentrated their accommodation on the central tower-, along with the current 'night shift' consisting solely of Helia sitting in her office, this was the best time to take action. Exiting the maintenance tunnel, John landed casually on his feet, closing up the tunnel behind him before he coughed to attract Helia's attention.

"What-?" Helia said, looking up from the computer that she had been studying to find herself staring at a man in a long black cloak and silver mask. "Who are you?"

"You may have heard of me," John said, looking solemnly at her; her surprise had been slight, but it was enough for him to confirm that she didn't know how he'd arrived here, which would hopefully increase the impact of his current message. "I am the man known in this galaxy as the Phantom of the _Ancestors_."

"Excuse me?" Helia said, her eyes widening at the additional venom placed on that final word. "You have been claiming-"

"I was _given _that name by other sources; I didn't set out to identify myself as something I wasn't at first, and I now have no interest in affiliating myself with your people directly after what you have done," John said, making his contempt clear as he looked at her; the fact that he wasn't officially 'designated' as an operative from Earth at least gave him the ability to tell this bitch what he really thought of her. "Parts of this galaxy have been waiting for your return for centuries to save them from the nightmare _you _released, and what's your response when you come back? Kick out the heirs to the kingdom and set up shop in a secure location that you feel comfortable in."

"This is _our _city-!" Helia began, standing up from behind the desk to glare at John.

"Because you built it; that only takes you so far, as far as I'm concerned," John said, his expression cold as he stared back at the Ancient captain. "You created the most incredible city this galaxy- maybe even several galaxies- have ever seen, and when you come back to find that someone else is using it, your automatic response is to kick them out?"

"Why should we not reclaim what is ours?" Helia asked.

"There's a difference between reclaiming what's yours and kicking people out because of a stupid sense of entitlement," John retorted.

"You want us to abandon this city to them?" Helia said, her gaze narrowing as she looked at the Phantom.

"I'll settle for you showing them the respect they deserve by letting them work here, but I'd be happy with you leaving as well," John replied in a dismissive manner; he really would have preferred them leaving, but he didn't want to give Helia any reason to be so scared of him (Assuming she'd admit to fear) that she turned violent to try and get rid of him.

"We _created _this city; what have they done apart from use what we have created?" Helia said, looking at him with that same arrogant edge that . "They have taken what we have conceived-"

"Because it was _there_; can you honestly say you wouldn't have done the same if some race older than you had created something that you managed to find?" John retorted. "Using what others have created shows sense, not laziness; they respect what came before and are willing to learn from it… and, quite frankly, they use it a _lot _better than you did."

"What?" Helia said, looking at her opponent in shock.

"You ran and bailed on this galaxy when the threat that you created was too much; you might have been justified in leaving, but when faced with a similar situation, Earth managed to come up with a means of continuing the fight and fending off the current Wraith assault," John said, still staring at her with a cold glare that clearly demonstrated the contempt he felt for her compared to her predecessor.

"What our peers did is of no concern right now; what matters is that _we _are here," Helia said, staring at the masked man. "I will _not _be ordered out of our city because you object to what we have done; we need time to adjust to this universe-"

"Which involves dismissing the people who saved your asses as useless?" John interrupted, the glare under his mask still as solid as the mask itself. "They helped you, and all you can do for them is tell them to get lost?"

"And what makes you think that they will simply be-?" Helia began.

"For the record, there's no point going to any of them about this," John interrupted, suddenly guessing where she might be going with her next statement. "I don't work for Earth, I do not take orders from them, and I am not officially affiliated with them; I just like them better than you."

"And I should accept this?" Helia asked, looking indignantly at him. "I should just… allow them back into _our _city-!"

"You should at least consider it," John said simply, looking coldly at her. "Keep in mind that they were under no obligation to let you kick them out- you don't exactly have the numbers to resist them if things turned ugly- and give thought to bringing them back into this city, because if you don't, I can make things _very _difficult for you…"

"And I should believe this?" Helia asked. "We _created _this city-"

"Which, the last time _I _checked, you've only inherited control of right now as the most senior ranking Ancient left alive; your knowledge of Atlantis prior to you getting lost out there is relatively limited," John pointed out with a slight smile. "I, on the other hand, have lived here for over twenty years and have spent that time learning all the ins and outs of this city; do you honestly think that you know more about this city as it is now than I do?"

He gave her a moment to think about his last statement, and then he turned around to face the door of her office-

"STOP!" Helia yelled, the sound of something being pulled out of something else giving John a clue to what she was about to do even before she fired, the Ancient pulse-weapon's blast dissipating harmlessly against his personal shield as he turned to look at her.

"Is that really what you've come to?" he asked, putting the right edge of scorn in his voice as he looked at her. "The most enlightened race in the universe, shooting at people because they made a few points you didn't want to hear?"

"I-" Helia began.

"Consider what I said, and I might have some respect for you," John said grimly. "As far as the future goes, I can promise you that, from this day onward, I will be the Phantom of Atlantis only; you have proven that the Ancestors are not worthy of any veneration or respect from anybody."

With that statement, John turned and ran for the office door, leaping over the walkway to land on the gateroom floor before he turned and ran for the inactive Stargate, diving through the window behind the Stargate to leap from the tower before Helia could catch him or call for assistance.

As he adjusted the cloak to glide to safety, heading for one of the lower buildings with a convenient hatch in the roof, the man known as the Phantom hoped that what he'd done wouldn't make matters worse for Earth; he'd publically declared his independence of them, and it wouldn't be hard for others to confirm that assessment, but it was still going to take a while to change the Ancients' minds…

But he _would _change their minds.

If nothing else, they would _not _discover the room where he had left Elizabeth's body before he was ready to show it to Elizabeth herself…

* * *

AN 2: Well, there you have it; further information about when John ended up in Atlantis has been disclosed, and the stage is set for the confrontations that will reveal the missing answers within the next few chapters…


	41. City in Peril

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: A predominately Earth-focused chapter this time around, as Elizabeth learns about recent events in Atlantis (Having not been kept as up-to-date as she was in canon because Sumner isn't as interesting in sharing things with her as Sheppard was)…

AN 2: Events in this chapter prompted me to realise an omission I'd made earlier, so I went back and made some changes to 'What's in a Name?' to clarify what happened to the _Orion_ when the Ancients came back; I apologise for any confusion this may have caused.

Mystery of the Phantom

Sitting around the table with the former heads of her medical and science department, Elizabeth tried not to show how much she was enjoying this opportunity; after spending the last few months at a loss, it was a welcome opportunity to talk with someone else about the Stargate and Atlantis who really understood what she was going through, as opposed to the various IOA 'debriefings'.

Among other things, she was glad to be able to talk to someone about how things were going negotiating with the Ancients in Atlantis; Carson's visit might have been a surprise, considering her initial lack of response to his attempts to call her, but when presented with the chance for this dinner, she'd welcomed the chance despite her initial reluctance.

Talking with Rodney and Carson had been awkward at first, given how long it had been since they'd seen each other- and virtually never in a social environment-, but after a while they'd fallen into a reasonably comfortable pattern, talking about their lives since returning to Earth as much as they could without risking being overheard. McKay had expressed his frustration at his new role in Area 51- apparently he actually resented working with people who treated him with excessive respect; she recalled a McKay who would have welcomed that kind of treatment-, and Carson had shared what he could about life at the SGC.

Carson had mentioned that there'd been a bit of an uproar a couple of weeks back about a confrontation between Helia and the Phantom, but after the Ancients had confirmed that Atlantis had no direct contact with the Phantom beyond him simply occasionally showing up to help them out, Helia had simply informed them that she would be resorting to additional security measures to try and capture him and left it at that. Woolsey was apparently concerned that the Phantom's actions had jeopardised the Ancients' thoughts on letting the expedition eventually return to Atlantis, but he was the only one voicing that opinion; Helia had even left them a message confirming that she understood that the Phantom was a rogue element…

That news was the only thing that left Elizabeth feeling glad that she was no longer directly affiliated with Atlantis; she wasn't obliged to tell the 'new' commander everything she knew about its primary guardian.

As Rodney and Carson fell into a talk about their current roles, Elizabeth took a sip of her wine and reflected on her private frustrations; the two men in front of her could move on, but even if she could find a job she appreciated half as much as she'd appreciated her time on Atlantis…

She allowed herself a brief, private sigh of frustration while she was sure the other two weren't looking.

Even if she could move on from Atlantis, she couldn't 'move on' from the masked man who'd informed her that she gave him something to live for in a galaxy that had given him nothing but things to die for.

She may not understand why John Sheppard felt that strongly about her, but how could she abandon the man who'd done so much for them, and then told her that it was all for her? She may not understand what she'd done to deserve such loyalty, but that didn't mean that she could just abandon it.

She would have believed that John deserved better even if she hadn't read about his past; the knowledge that he'd had such an apparently tense relationship with his family back on Earth just made it more personally important to her to ensure that he knew she hadn't abandoned him.

She wished that she could just find a simple solution to a simple problem for once; things seemed to be becoming increasingly complicated, and she was no closer to finding a solution for any of the problems in front of her than she had been when she arrived on Earth. Atlantis's fate had been taken totally out of her hands, which also put a neat hold on her ability to talk with John about her revelation, and she certainly wasn't about to tell Helia a thing about him.

She'd thought about visiting John's family for more information- his mother had died a while ago, but he still had a living father and a younger brother-, but had dismissed it; without any evidence and only a theory that the John Sheppard she had discovered was 'their' John Sheppard- to say nothing of how classified the true explanation was and her own ideas about how he'd ended up in Pegasus being nothing but theories rather than definite facts-, she wouldn't be able to do anything other than create an awkward situation.

"Elizabeth?" Carson's voice said, breaking Elizabeth's train of thought as she turned to face him, the Scottish doctor looking anxiously at her. "Are you all right?"

"I'm fine," Elizabeth said, smiling back at him. "It's just… it's getting late, and I've been catching up on my sleep."

"Oh," McKay said, apparently taken aback at that statement.

"Thank you," Elizabeth said, reaching out to put a hand on Carson's arm. "I appreciate you getting me out."

"It was nothing," Carson said, smiling back at her, only for the warm mood to be broken as Elizabeth and McKay's cellphones suddenly all started ringing, the former Atlantis staff exchanging grim glances as they pulled out their phones and answered them.

Elizabeth only needed to hear General Landry's voice on the other end to know that things had just become _very _bad…

* * *

The race back to the SGC to respond to Landry's query had gone by so quickly Elizabeth wasn't sure she'd ever be able to remember the actual journey; after hearing that a crisis had emerged on Atlantis, the only thing that mattered to her was getting to the briefing room, where she, Carson and Rodney had just enough time to exchange greetings with the already-present Sumner before General Landry walked in.

"We got this data burst about twenty minutes ago," Landry said as he walked across the room, grimly activating a screen on the briefing room wall. As Elizabeth watched, the screen displayed a poor-quality recording from Atlantis's control room, filled with static, sent by General O'Neill, Woolsey's barely-visible form standing behind him with what looked like a gun in his hands.

"_Atlantis is under attack from Replicators_," the General's voice said; it was slightly tainted by the static of the recording, but the words were still fairly clear. "_Somehow they figured out how to override their programming. The Ancients were taken off guard and have lost most of the city already__. Request immediate evacuation_!"

"_They're coming_!" Woolsey yelled after firing his gun at something off-screen, turning back to General O'Neill just as the recording stopped, turning the attention of the city's former senior staff back to Landry.

"They never made it to the gate," Landry confirmed, giving the four people before him a moment to process that news before he continued speaking. "I was informed they had a law written into their base code that made it impossible for them to harm the Ancients. How the hell did this happen?"

"It is… remotely possible…" McKay said, looking awkwardly at Landry after receiving a hard stare from Sumner, "that in trying to rewrite Niam's base code, I… uh, we, may have opened the door for them to make other changes."

"_You _did this?" Landry said.

"At the time we thought it was the only possible way to save the city," Elizabeth said, looking firmly at Landry; the consequences were shocking, but they had also completely unpredictable at the time they'd taken action.

"We can assign blame later," Sumner said firmly. "Right now, our priority is determining how to respond to this problem; _Daedalus_ and _Orion _are already en route, but we need to identify the best way to get a nuke through the city's shield-"

"Hold on; you're planning to _nuke _Atlantis?" Rodney said, looking indignantly over at Sumner, clearly unable to believe what he was hearing.

"It's the gateway to Earth," Landry said, his tone firm.

"And we have an iris!" Rodney protested, indicating the Stargate visible from the briefing room.

"Yes, we do," Landry said, "but thanks to your Intergalactic Gate Bridge, all they have to do is rewrite your macro and they can come out anywhere in the Milky Way."

"Yeah, but those macros are very complicated," Rodney tried to protest.

"_They _are very complicated, Doctor McKay," Landry countered. "They just rewrote their own damned base code! I think they can handle it."

"Why are we even talking about this?" Elizabeth asked, looking firmly at Landry; he might have made a valid point, but she had a few points of her own that she wanted to make in this situation. "General Landry, even if the Ancients are lost to us, General O'Neill and Mr Woolsey may still be alive, to say nothing of what Atlantis has to offer in itself; if we could be provided with a marine contingent and Colonel Carter's new Anti-Replicator weapons-"

"I'm sorry, Doctor Weir," Landry interrupted. "I appreciate your continued interest in what Atlantis has to offer us, but I have standing orders. They happen to be _General O'Neill's_ standing orders. The _Daedalus_ will be there in a little under four days. Now, how do I get a nuke past their shield?"

As Sumner began to voice his own personal theories about the most appropriate location to target, Elizabeth glanced over at the other two doctors sitting around the table right now, and was relieved to see them looking at her with what she could best describe as apprehensive certainty.

They didn't know how they were going to pull it off in specific terms, but the three of them were all already prepared to find some way back to Atlantis, regardless of what rules they had to defy to do it.

It was almost surprising how quickly they were all agreed that Sumner wouldn't be informed about this- not only was nobody even reaching over to attract his attention, she was fairly sure that McKay was trying to make sure that the colonel wasn't even looking at them-, but it was clear that all three of them understood the reasoning behind that decision; Sumner was too bound by the rules to go along with something this big.

There had to be _something _that they could do; Elizabeth was _not _going to let John die because they'd made a mistake that put the city he had protected for so long in the line of fire with him still in it…

* * *

Crouching in the maintenance tunnel as he heard the sounds of fighting being waged around him, John wondered what was more disturbing; how little he really minded the fact that the Ancients were dying, or how fundamentally stupid their military tactics seemed to be.

He could just about accept the fact that they hadn't had much in the way of anti-Asuran weaponry because they would have assumed that the Asurans would just stop once they were ordered, but they didn't seem to have taken any steps whatsoever to shoulder up Atlantis's defences (He hated to admit it, but he was selfishly grateful that _Orion _had been in the Milky Way when the Ancients showed up; the ship might have been useful in this fight, but he doubted that it would have delayed the Asurans for long given its limited drone supply and some parts still not operating at their best). Not only were the Asurans able to bypass Atlantis's shield with frustrating ease- probably something about their ship being Ancient technology as well-, but they were practically steamrolling over the city; the Ancients had managed to launch some drones at the attacking Asuran ship, but all that had accomplished was halting the aerial bombardment in favour of a more direct assault.

As it was, the Asuran ship they'd sent had been forced to land due to engine damage, but the ship's crew had come through undamaged, marching through the city and killing the Ancients with an efficiency that fit their machine-like natures; they were just breaking necks or punching through chests of any Ancient they came across in a cool, methodical manner.

In some ways, the swiftness of their attack made it easier for John to make a decision on what to do next; he might have been tempted to at least try to save the Ancients out of human decency, but with the Asurans so focused on eliminating the Ancients, it made his choice easy.

There was no way to protect the Ancients- now that the Asurans knew that the 'parents' who'd abandoned them had returned, they weren't going to stop until they'd annihilated all of them-, but Richard Woolsey and General Jack O'Neill might just be able to slip under the radar long enough to get to safety, particularly since they wouldn't match what the Asurans were looking for; O'Neill might have the ATA gene, but John had learned over the years that there were still enough subtle differences between Ancients and ATA-positive humans to make a difference when running a scan for Ancient life-signs compared to human ones.

In other words, right now his main priority was to track down the only two Tau'ri left on Atlantis and get them somewhere safe until they could come up with a better plan of attack; Woolsey might be a bit of a jerk, but he'd made the right call when it counted more than once, and O'Neill _definitely _didn't deserve whatever the Asurans would do to him.

Checking his pockets to ensure that he had everything he might need, John took a deep breath and began to crawl through the tunnels; all he could do right now was hope that the Asurans were as ignorant of the fine details of Atlantis's construction as the Ancients had been, and that the people he was looking for were still alive…

* * *

Elizabeth couldn't believe that she was doing this; after years of working with the system, she was defying virtually every oath she'd taken and attempting to rescue a potentially lost city with a group of five people, over half of whom weren't trained soldiers?

The only thing more shocking than that was how easy it had been to make such a decision in the first place. She might be willing to take orders, but she'd learned after arriving in Atlantis that sometimes you had to go against what people wanted you to do in favour of what you needed to do.

On the brighter side, they at least had some kind of plan for getting back to Atlantis, but the finer details still needed some work. The Anti-Replicator weapons, colloquially known as ARGs, were at least simple enough to use- according to McKay all you had to do was point, fire, and the Replicators would collapse-, and McKay had assured them that he had a means of getting them through Atlantis's shield when they were ready to head back to the city, but even with Carson willing to pilot the gateship, that had still left them with the issue of getting access to the ship without the SGC closing the Iris until McKay had some up with his plan.

Elizabeth still couldn't believe that she'd had to flirt with Doctor Lee to give McKay time to add a keycard to the authorised list; it wasn't that he was a bad person, but something about it just felt… _wrong_…

Still, none of that mattered now; what mattered was that they'd put together everything they needed for their unofficial mission, and they were now sitting in the gateship, ready to take action. She felt awkward dressed in the black BDUs they'd picked up for this mission, but her usual attire would have hardly been suitable for this kind of mission, and it was only a one-off anyway.

On the bright side, getting to the gateship had been straightforward enough, and Carson seemed relatively comfortable in the pilot's seat despite his obvious apprehension, leaving them with nothing more to do than let McKay dial the Stargate and let them leave.

"We're ready!" McKay said, hurrying into the gateship's rear hatch.

"Let's go," Elizabeth said, nodding firmly at Carson as the hatch closed behind them.

"OK, they'll be able to get through my hack pretty quickly," McKay said.

"We don't need much time," Carson said, despite his apprehensive expression suggesting that he wasn't as confident as he was trying to present. "We're going down now."

As the gateship lowered into position before the Stargate, Elizabeth briefly heard Landry's voice ordering them to stand down, but she ignored it; she had more important things to deal with right now.

As they dived through the Stargate, Elizabeth smiled in relief as she felt the rarely-experienced but long-missed thrill of travelling through the wormhole.

_I'm coming, John_… she thought.

She didn't care what the consequences of this action would be for her long-term career; after John had saved them all so many times, it would just feel wrong if she didn't at least try to save him in return.

* * *

"My turtles!" Carson yelled, after they had been sitting at Midway Station for a few as McKay worked on his console.

"What?" Elizabeth asked, looking at him in surprise; of everything her former chief doctor could have said, that certainly hadn't been on the list.

"I just bought some wee baby turtles and no-one knows to feed them," Carson explained.

"Well," Elizabeth said, stuck for anything else to say to such an out-of-the-blue comment, "turtles are pretty hardy. I'm sure they'll be fine."

"I figured I'm back for good so I might as well get a pet," Carson explained, apparently feeling a need to explain now that he had brought the matter up. "I'm allergic to cats and, well, I'm at work too long to be fair to a dog, so I went with turtles. I've probably killed them."

"They'll be fine," Elizabeth said, stuck for anything else that she could say to that statement before she looked at the gateship's other resident. "How are you coming along, Rodney?"

"Oh, trust me, I am going as fast as I can!" McKay said, looking at her in frustration.

"Poor little buggers," Carson said, evidently still lost in thought over the turtles.

Elizabeth was spared from having to think of an appropriate response to that statement- she sympathised with Carson's plight as a pet-owner herself, but this wasn't the time to think about that- when the gateship's HUD activated, displaying a grid pattern with some numbers that Elizabeth thought she understood…

"The Milky Way gate just activated," Carson said, looking apprehensively at her and John before Colonel Sumner's face appeared on the screen.

"_Doctor Weir_," the colonel said, his expression grim as he looked at them, "_I'm fully aware that you, Doctor McKay, and Doctor Beckett are in that gateship, and I'm also aware of what you're trying to do. I would like to commend you for your courage, but the fact is that what you're attempting is foolish at best; Atlantis is lost and we have our orders to ensure Earth's protection. I respect what you have accomplished during that mission, but the mission is over; if you don't come back to the SGC _now-"

Remembering some of her past experience at travelling in gateships, Elizabeth hit the button to terminate the connection, no longer interested in hearing what Sumner had to say.

"Well," Rodney said, looking up from his work to exchange glances with the other two, "I think it's probably safe to assume he won't be interested in coming back."

"We defied orders and went against everything he believes we need to survive out here; I don't think Colonel Sumner will be willing to work with us again any time soon," Elizabeth said grimly.

It was slightly sad to know that such a long-term relationship had just been ended, but it was still just a professional relationship rather than a friendship; none of them had ever really connected with Sumner on anything more than a professional level, and that was unlikely to have changed at any point in the future. He had been a good ally in their time in Atlantis, but even as the science teams and their remaining Athosian full-time team members had come to see Atlantis as a home, Sumner had all but forced the military to maintain a professional distance from the rest of the population, treating Atlantis as a place of work rather than a home.

Elizabeth had kept him on because she had no legitimate reason to fire him, but she wasn't going to object if he decided to leave even after they'd recovered Atlantis (And they _would _take the city back; the alternatives were unthinkable).

Losing Sumner would be an inconvenience, of course, but if all went well, maybe Elizabeth would be able to use General O'Neill's backing to nominate her own preferred candidate for the head of Atlantis's military…

Her speculation ended as McKay's console let out a more positive-sounding beep.

"OK, I've got it," the Canadian physicist said, looking up at them with a slight smile.

"Last chance to change our minds?" Carson asked, looking over at the other two before he nodded in grim understanding at the lack of response. "Let's go, then."

As they dived through the wormhole that would take them back to the Pegasus Galaxy, Elizabeth couldn't stop herself from grinning at the thought of what was waiting for her at the other end, the grin remaining on her face even as the ship emerged in a forest-covered world.

"We're here!" Carson said, looking back at them with a smile.

"We're sure about that?" Elizabeth asked, looking over at Rodney; she didn't have any real doubt that her chief scientist would have chosen the right address, but she had to be sure.

"I reconfigured the macro to take us to the Athosians' new homeworld; if Teyla and Ronon aren't here, someone's bound to know where they are instead," Rodney said as he got up from his seat. "Let's just… go and find them, huh?"

Elizabeth honestly couldn't blame Rodney for wanting to keep moving; they were committed to their current course of action, but if they stopped to think about what they'd done for too long they might just end up panicking about the odds against them and be in even _more _trouble…


	42. The General and the Phantom

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: To whom it may concern, I'll be focusing more on the Phantom rather than Elizabeth's team at this point in the story- what they'll be doing is fairly similar to what they were doing in canon, such as picking up Niam and returning to Atlantis, so the absence of Sheppard doesn't really have enough impact to make it interesting-, but that will shift when the time is right, I assure you…

Mystery of the Phantom

Crawling through the tunnel, John tried not to think about how close he'd come to being detected by the Asurans; he _really _didn't need to know how low on power his personal shield was. With him having to turn it on to deflect his life-signs every time an Asuran came too close to him- he wasn't clear on what the Asurans were capable of detecting on their own, so anything he could do to minimise the signals he was giving off would probably be a good move-, he was running out of power for what may be a meaningless precaution, and he didn't know how much longer it would take for him to get somewhere safe enough for him to take a break.

_Safe_…

_Damnit_, he thought to himself in frustration. _I spend over two decades keeping this city safe, and then the original owners come back and it falls apart after six weeks_.

Atlantis was meant to be _completely _safe, he shouldn't have to worry about even _parts _of it being dangerous-

The sight of movement caused him to stop, but when he saw an older man in green combat BDUs who could only be General Jack O'Neill walking along the corridor, too stealthy and quiet to be an Asuran, John didn't need long to make his decision. Slipping out of the nearest access panel, he landed on the ground and took a couple of steps forward.

"General Jack O'Neill, I presume?" he said, smiling slightly at the other man as the general in question started in shock at the sound of his voice, aiming his gun at John with a speed that John had to admit was impressive in a man of any age.

"Who the…?" General O'Neill said, looking at him in confusion for a moment before inspiration dawned. "You're that Phantom guy, aren't you?"

"The Phantom of Atlantis, at your service, General O'Neill," John said, taking hold of the edge of his cloak with one hand to give his bow an extra flourish before he stood up and looked at the other man with a slight smile. "I assume you've heard of me?"

"A few things," O'Neill said, looking at him with a neutral expression. "You've had an… interesting life, if nothing else."

"It's given me some equally interesting skills," John replied. "And right now, General, you and Mr Woolsey are going to need those skills if you're going to survive this."

"No offence, but I don't think even you can get us out of this," O'Neill said, sighing as he looked back the way he'd come; the fact that he took his eyes off John at least suggested that he trusted the other man, but that was small comfort considering what they still had to deal with. "SGC's under standing orders to nuke Atlantis if it falls under control of a hostile force."

"Oh," John said, resisting the automatic urge to yell at Jack about that particular decision- it made sense on a _practical _level, even if he didn't like it- and turned his attention to the more immediate issues he could deal with. "So… what were you doing there?"

"Grabbing some food and conducting recon," Jack replied, briefly opening a picket to indicate a few energy bars before zipping it up again. "Stargate Operations is crawling with these guys, so we're not going to be able to get out that way…"

"In other words, we're stuck until Earth either blows us up or we find some other way out," John said, looking grimly around himself at the corridor they were currently standing in before he turned to look at Jack. "I _might _be able to get us to a gateship bay so that we can evacuate, but I want you to be clear that if there's any way for us to save Atlantis-"

"Place is your home; I'm not going to begrudge you if you think you can stop it blowing up," O'Neill said, before he looked more pointedly at the other man. "Just so long as you're clear that I'll stop you if I think what you're doing is going to endanger us or Earth."

"Understood," John said, before stepping back slightly and looking hopefully at O'Neill. "Well, your guy's still missing; lead on."

With O'Neill leading the way, the two men continued to walk along an increasingly-damaged corridor, the lights growing obviously dimmer the further they went, until the sound of a voice whispering anxiously reached their ears.

"And if I'm a Replicator?" O'Neill said as he walked up towards the source of the voice, revealing the suit-wearing form of Richard Woolsey, awkwardly holding a gun in a manner that made it clear he had no real idea what to do with it as he peered around a corner.

"Then I just gave away my position," Woolsey said, having the decency to look guilty about his mistake before his eyes fell on the figure behind the general. "What-?"

"Richard Woolsey, meet… the Phantom," O'Neill said, indicating the masked man with a brief wave of his hand as they walked into the battered corridor, various items of furniture overturned. "He's offered to help, we're not exactly in a position to say 'no', so here we are."

"I see," Woolsey said, clearly stuck for anything else to say as O'Neill tossed him an energy bar, at which point he decided to focus on more personal matters than the presence of a man the IOA didn't officially like. "Thank God, I'm starving…"

"Make it last," John said, looking pointedly at Woolsey. "We don't exactly have much in the way of options right now, and then there's all the Asurans hanging around here…"

"That's an understatement," O'Neill said grimly. "Stargate Ops is crawling with 'em; we're not getting out that way."

"Are they looking for us?" Woolsey asked.

"No way to be sure," John said grimly. "With the life-signs detectors out of action in these areas, it's possible that they don't know there's anyone here to look for, but we can't exactly afford to underestimate them."

"And then there's the bomb," O'Neill pointed out.

"Bomb?" Woolsey said, looking sharply over at the general. "What bomb?"

"Landry has standing orders to nuke the city if there's any sign of a foothold situation," O'Neill said, at least having the decency to look awkward about that information.

"What kind of a standing order is that?" Woolsey said, looking incredulously at the older man.

"His," John said, grimly indicating the general before he held up his hands defensively as Woolsey looked between them in shock. "I don't like it either, but I get where he's coming from; if Atlantis is really lost to enemy forces, too many people would suffer if nobody at least _tried _to destroy it."

"And you have no objection to the fact that we're _in _it?" Woolsey said.

"I'm going to do what I can to ensure that it doesn't come to that," John said, looking firmly at Woolsey for a moment before he sighed as he leaned against the wall. "I just need some time to think of a plan…"

"Didn't you mention a gateship bay-?" O'Neill began.

"Getting out of the city just keeps us alive; I'd prefer a plan that will let us save Atlantis at the same time," John pointed out.

"Well, unless you've got an army in your pockets, I don't think-" O'Neill began.

"_Authentication code Alpha One Delta Sierra Niner_," a familiar female voice suddenly said from O'Neill's pocket. "_General O'Neill, Mr Woolsey, do you copy_?"

"Doctor Weir?" O'Neill said, pulling his radio out of his pocket and turning it on, thankfully missing the smile on John's face as he heard the voice he'd been wanting to hear again for months. "Is that you?"

"_Yes it is_," Elizabeth's voice replied. "_I'm sorry for being abrupt, but we need to know if you're anywhere near Stargate Operations_."

"We're not," John said, before O'Neill could say anything; maybe the older man would consider it rude, but after he'd spent weeks not hearing Elizabeth's voice, he wanted to let her know that he was still alive.

"_That's… good_," Elizabeth said (Was it John's imagination, or did she sound more relaxed than she had earlier?). "_We'll get back to you later, General; Weir out_."

As the connection terminated, the three men exchanged brief glances before a loud explosion shook the corridor they were standing in. Hurrying over to a door that he knew led to a room with a convenient window- he might not have accessed much of the database, but he knew where things were well enough-, John reached the window in time to see a gateship flying away from the central tower as it burned brightly, parts of it damaged by what appeared to be a fairly substantial explosion, one of the side towers collapsing as smoke and flame burst through the upper levels.

"What was that?" Woolsey asked, walking into the room and looking out of the window in confusion, his eyes widening at the sight of the damaged tower. "Is Doctor Weir attacking the city?"

"She'd better be," O'Neill said, nodding in thoughtful approval.

"Why can't she get back to us for two hours?" Woolsey asked, frowning.

"I don't know," O'Neill said.

"No immediate ideas here either," John said, looking apologetically over at the other two men as they turned to look at him, before his eyes narrowed as he looked at them in an authoritative manner. "However, if we can focus on staying alive right now, that's the main thing; the Asurans are going to be busy dealing with the damage to the control tower, but they may have detected that radio communication before everything went down, so we should use this opportunity to get to a more secure location while they're distracted."

"What makes you so sure they'll be distracted?" Woolsey asked.

"They want Atlantis to get to Earth, Mr Woolsey," John said, looking firmly over at the other man. "That means they need the Stargate, which means they need the control room to be fully operational; do I need to spell the rest of it out?"

"Check," O'Neill said, nodding at him in understanding. "Lead on."

This might be their first meeting, but so far, John was definitely enjoying the chance to talk with General O'Neill; everything he saw of the man only further improved the assessment of him he'd formed based on Elizabeth's old stories…

* * *

"That sounded like another explosion," Woolsey said, as another loud noise- albeit significantly quieter than the previous one- reached their ears after a period of silence, the three of them only occasionally talking to limit the risk of being caught. They'd been walking through the damaged portions of Atlantis for a while, John wanting to keep them on the move while not wanting to go too far from their original location in case they accidentally encountered a working scanner, but that was the first sign of any additional activity in the rest of the city.

"Yes," O'Neill said, nodding thoughtfully at Woolsey. "Yes it did."

"What does that mean?" Woolsey asked, looking urgently at the other two.

"Something exploded," O'Neill said, in the same calm voice.

"But is it our team attacking the Replicators, or the Replicators attacking them?" Woolsey asked, still sounding obviously flustered at this turn of events.

"We'll probably find out sooner or later," John said, attempting to sound nonchalant about it; he was as curious to learn the answers as anyone, but was trying to focus on what he could control rather than what he couldn't answer at this time.

"How did they even get here?" Woolsey said after a moment's pause. "Through the gate?"

"We've been right next to you since this started, Woolsey; how the hell are we meant to know those answers if you don't?" John pointed out, as O'Neill closed his eyes in frustration at the other man's questions.

"Look," Woolsey said, putting the gun down and practically tearing his tie off in frustration, "I _told _you I wasn't good at this-"

"They'll be back soon," John said firmly; the man might not be much use, but the last thing he needed was for oneo f the people he was trying to keep alive to have a breakdown. "We just need to stay on the go and out of danger until they get back to us…"

The man in the mask tried not to think too much about the implications of the explosions they kept on hearing taking place outside in other parts of Atlantis; he doubted that Elizabeth and her team would be so casual about attacking the city, which suggested that the Asurans were the ones firing weapons right now, but that still didn't give him much hope about their ability to evade for long.

He hated to be pessimistic, but he had to face the facts; if Elizabeth was on this team, it was unlikely to be an SGC-sanctioned operation, which meant that it was unlikely they had any fully-trained pilots on board their gateship, which meant that they'd be relying on luck and whatever natural skill their current pilot had to get to safety…

As further explosions rocked the city, he could only keep walking and hope that Elizabeth and her team would survive this mess…

"They're overdue," Woolsey said.

"Life doesn't exactly operate on a schedule, Mr Woolsey," John said, turning around to glare at the other man. "If you don't like unpredictability, I apologise, but we can't always accommodate your need for exact detail; this is the real world, and stuff _happens _in the real world that doesn't always happen on a timetable."

It was abrupt, but he wasn't going to treat this man with kid gloves no matter what the long-term consequences might be regarding his presence in Atlantis; their priority right now was staying alive, and that was what he was going to make sure they focused on.

"_Hello_?" Elizabeth's voice said over the radio at last. "_General O'Neill? Phantom? Are you there_?"

"We're both here, as is Woolsey," O'Neill said, pulling his radio out of his pocket as the other two men gathered around him. "Doctor Weir, can I ask what took you so long?"

"_We had to pick something up in space; getting back was… more complicated than we'd anticipated_," Elizabeth replied.

"And you're currently… where?" O'Neill asked.

"_Heading for an underwater gateship bay_," Elizabeth replied, prompting a slight smile from John; he was fairly sure he knew which one she'd be heading towards, considering that he had 'introduced' them to an underwater bay during that incident when he'd been tracking the hives…

"Neat," O'Neill said, before he continued. "And talking of interesting news, may I express my… _surprise_ that Landry would send you on a mission like this?"

"_Well, sir_," Elizabeth said- to her credit, her tone was as casual as it always was, despite the news she was disclosing-, "_General Landry didn't sanction this mission_."

"So," O'Neill said, looking at John with a foreboding expression, "am I to assume you are _not_ surrounded by heavily-armed S.G. teams and young strapping marines?"

"_You've got myself, Ronon, Teyla, Doctor McKay, and Doctor Beckett_," Elizabeth replied.

"Oh, Doctor Beckett!" O'Neill said. "Well, _I'm _comforted-!"

"Any help in this situation is appreciated, El- Doctor Weir," John said, hoping that nobody else noticed his slip-up; he was so used to talking to Elizabeth in private he'd almost forgotten that they weren't alone this time.

"_We do have a plan, General_," Elizabeth said, McKay's voice heard in the background saying something about a lock. "_We'll fill you in on as soon as we're sure it's safe_."

"Yeah, I'm sure you do," O'Neill said. "But just so you know, Doctor Weir, in the event-"

"She won't," John said before he could stop himself.

"Excuse me?" O'Neill said, looking critically at him.

"She won't fail," John repeated, committing himself to his current course of action as he looked at the general; as with Woolsey, making a good impression might be important, but he also wanted to ensure that everyone present knew him for what he was. "I've seen Doctor Weir in action as leader of this city, General; she might make questionable decisions, but she wouldn't take risks without a plan."

"Well," O'Neill said, looking at the now-silent radio in his hands- he must have turned it off when he turned to talk to John- before he sighed and shrugged, "looks like we're in her hands now anyway."

"And why do you have such faith in her?" Woolsey asked, looking curiously at the masked man. "As I understand it, you've been an independent operative in this galaxy for years-"

"Things change," John said pointedly, as he looked at Woolsey; regardless of the situation they were in or how Woolsey would react, that was one thing he wasn't going to reveal to _anyone _else until he'd had the chance to tell Elizabeth about it. "Maybe I'll answer that question once we get through this."

He just hoped that his attempt at projecting confidence was successful; regardless of what Elizabeth had planned, they weren't exactly faced with brilliant odds right now…


	43. Reunion

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Mystery of the Phantom

"_Hello_?" a voice said from the radio after the three men had been walking in silence for a few more minutes, John subtly moving in the direction of the underwater bay they were most likely to be using while trying not to make it too obvious that had a more definite plan in mind…

"Yeah?" O'Neill said, as he answered the radio. "How's everything going with that plan of yours, Doctor Weir?"

"_Actually, General_," Elizabeth said, her voice displaying her discomfort at this turn of events, "_we're going to need a favour_."

"Oh?" O'Neill said, exchanging brief glances with John and Woolsey before returning to the conversation. "What kind of favour are we talking about here?"

"Well," Elizabeth began, "_we made it to the underwater jumper bay we thought was there, but unfortunately, while the outer door worked, the inner door is remaining sealed as we can't drain the water level, and we apparently suffered some minor damage during our return that's left us with a leak in the gateship_."

John cursed the further evidence of the city's sudden run of bad luck; the Asuran attack must have damaged the automatic control systems for that bay- they'd taken a few knocks over the years and he'd only ever bothered to perform limited repairs on them because he'd tended to use the Stargate to get anywhere-, which meant that Elizabeth's team's chances of getting out on their own were shockingly limited unless he stepped in somehow…

"OK…" O'Neill said, looking thoughtfully at the radio. "I get what the problem is, but I don't get what we can do about it…"

"_We need you to get to the manual override in the gateship bay's control room and activate it so that we can drain the water out_," Elizabeth replied. "_We'd do it ourselves, but we can't open the gateship without letting the water in, and the outer door seems to have jammed since we entered it, so we can't get out that way_…"

"I know where that control room you're talking about is; we're on it," John said, reaching over to take the radio from O'Neill with a brief apologetic glance at the general; he might as well reassure Elizabeth about this latest dilemma personally. "Just hold on, Doctor Weir; we'll be there soon."

"_I know_," Elizabeth replied, that warm tone in her voice that he'd heard so often when they were alone, talking about nothing in particular…

"OK," he said, handing the radio back to O'Neill as he looked firmly between the two men, "we've not got far to go until we get to the control room they're talking about, but we also have to assume that the Asurans are going to work out what's happening sooner rather than later; the sooner we get there, the sooner they're out and able to help us."

"Not the greatest plan in the world, but I've heard a lot worse," O'Neill said with a slight shrug. "So, since you know the way… lead on?"

"You're _trusting _him-?" Woolsey said, looking over at O'Neill incredulously.

"Trusting the guy who's lived in this city for decades, hasn't done a thing to hurt us since we got here, and doesn't want to get caught by the Replicators any more than we do?" O'Neill retorted, pausing in thought for a moment before he nodded. "Yeah; I'm trusting him."

"Thank you, General O'Neill," John said, nodding briefly at the other man before he turned back to the corridor before him. "Come on; let's move."

* * *

After a few minutes of hurried movement- John couldn't quite call it 'running' as he'd had to adjust his pace to compensate for Woolsey's lack of physical condition and O'Neill's greater age, even if he'd never tell the other man that he was old to his _face_-, they finally reached the hatch that John recognised as the entrance to the control room for the underwater gateship bay, a ladder extending down towards it.

"So, this it?" O'Neill asked, as John paused to crouch down beside the hatch.

"That it is," John confirmed with a nod at the older man as he opened the hatch, only for his slight smile to falter as he found himself faced with water reaching up to the ceiling of the room below. "_Damnit_…"

"Let me guess; we need to go in there?" O'Neill asked.

"Bingo," John said grimly, as he reached up to shrug off his cloak, handing his gun over to the general as he tossed his cloak to Woolsey. "You might need this if any of the Asurans show up; it's not one of your anti-Replicator weapons-"

"You _know _about those?" Woolsey interrupted, looking at John in shock despite the cloak in his arms.

"I've been hanging around this city for years and the Asurans have been one of the hot topics of discussion for the last couple of months that the expedition were living here; I _think _we can assume I overheard _something _about that weapon over that time," John pointed out with a firm glare before he looked back at the other man. "The point is, tht gun won't stop them for good, but it should immobilise them for a few moments. I'll try and be as quick as I can, but it's still going to take a while; if I recall correctly, these controls are on a dead man's switch-"

"As in, you'll have to hold them down to work?" O'Neill said, looking at the masked man with new anxiety. "Isn't there a risk that you could… I dunno…"

"Drown?" John finished for him, smiling slightly as he tapped the mask and allowed the general to see the brief green glow surrounding his face. "This provides me with some additional air reserves; I wouldn't like to go for a long swim, but a relatively quick dip like this should be fine."

"So long as you're sure," O'Neill said after a brief pause, looking grimly at the water below them. "I know _I _wouldn't like to swim in that…"

"I'll be fine," John said, moving to crouch down beside the open hatch before looking back at the other man with a grim smile. "Just keep the gun ready if something shows up."

With that said, he took a deep breath and dived into the water, opening his eyes as soon as he was fully submerged. The oxygen in his mask also provided him with small 'goggles' so that he could see what he was doing more clearly than otherwise, and the oxygen also helped him stay underwater long enough to do what had to be done. After swimming along for a few moments, trying not to think about how cold the water was- he'd been a competent swimmer back on Earth, but this was a longer distance underwater, in colder temperature, weighed down by wet clothing-, briefly noting the window showing the gateship bay before he turned around to face the control console. Quickly scanning the various panels before him, John soon identified the appropriate lever on the panel on the other side from the window, pulling it down and holding it in position until the water level in the gateship bay had gone down to nothing. Swimming back to the surface, he emerged with a relieved smile, deactivating his mask's force-shield as he looked at his current allies.

"It's done," he said, hauling himself out of the water and taking his cloak back, pulling his Ancient shield device out of his cloak and placing it on himself after making a brief adjustment so that it could push the water away from him.

"They're in?" O'Neill said, as he handed the cloak back to the other man.

"Should be, anyway," John confirmed as he shrugged the cloak back on. "Door's open, they're coming in; all that we need now-"

John's thoughts were cut off when the door behind them opened once again, revealing a small group of five Asurans, each one aiming a weapon at them.

"_Crap_!" O'Neill said, firing his gun at them despite the obvious futility of such an action, Woolsey pulling out his own pistol to fire off some bullets that would have done little damage even against an opponent that would actually be hurt by them, until John fired his own weapon at them. The subsequent attack did little more than freeze the Asurans in place, but that was enough for the three humans.

"Neat trick," O'Neil said, glancing over at the Phantom. "I don't suppose that killed them?"

"As I said, all I can do is immobilise them," John said apologetically as he glanced at his weapon. "I read about your own anti-Replicator weapons, but without a working example I couldn't make this generate the same blast, so we've probably taken them down for a few moments at most…"

"Right," O'Neill said, nodding solemnly at him. "In that case, you hurry off and then find some way to double-back to that underwater gateship bay to give Doctor Weir's team some back-up; we'll try and make a fuss at this end to buy time."

"_What_-?" Woolsey and John said simultaneously.

"Hey, you're the expert in dealing with stuff in this city; best will in the world, I don't know enough about this place to be useful to them right now, so we're more use to you making a lot of noise the other way," O'Neill said, looking at John with a slight smile before he looked back at Woolsey. "So, let's focus on running and give the three docs and the three natives time to do whatever they came here to do, OK?"

John tried not to feel too uncomfortable about the general's automatic assumption that he was a native of the Pegasus Galaxy; he had more immediate priorities, particularly since Elizabeth was the only person who knew that right now anyway.

"If you're sure…" he said, looking uncertainly at the general; he didn't want to leave the other two men on their own, even if he acknowledged the tactical merits of General O'Neill's suggestion.

"I'm sure," O'Neill said grimly, indicating the door at the other end of the corridor they were standing in. "Go."

Refusing to give himself time to hesitate, John turned around and ran for the door, his mind already tracing the route to the underwater gateship bay that Elizabeth and her team would have entered by.

He'd just have to hope that the Asurans would want to use the general as a hostage- Woolsey he was honestly so-so about; he didn't want the guy to die, but he wouldn't feel that bad if he ended up dead either- and take it from there…

* * *

As she got out of the gateship, Elizabeth couldn't believe how complicated things had been; she knew that people always said that no battle plan survived contact with the enemy, but it seemed like they'd encountered at least half of the plan's potential problems fairly quickly.

The attempt to bomb the central tower and disable Stargate operations had worked, and they'd recovered Niam fairly easily despite Carson's concern about his ability to handle the ships- his piloting experience had naturally been limited ever since more men became available and Sumner decided that providing lessons to ensure that everyone who could fly knew how to do so wasn't a priority-, but with the cloak damaged and the need to get up close to the city to transmit the signal without reactivating Niam, they had been forced to retreat into this gateship bay to escape destruction.

McKay was still working on transmitting the program through Niam without bringing him up to a power level where he'd be a danger, but the fact that they hadn't heard anything else from General O'Neill, Mr Woolsey, or the Phantom didn't bode well for anything they might try to accomplish in this city…

As though summoned from her thoughts, John suddenly appeared at the now-open door of the gateship bay, dressed in his usual mask and cloak, gun in his hand and a tension in his stance that suggested that he'd been running recently.

"_The Phantom_?" Carson said, looking at the new arrival in shock as the rest of the team filed out of the gateship, holding on to their ARG weapons.

"That's me," John said, nodding grimly at the doctor before he looked over at the gateship, where McKay was still crouched down beside Niam's immobilised form. "What exactly is _that _doing here?"

"Trying to use him to transmit a code that will shut down the other Replicators without giving him so much power that he wakes up and tries to kill us all; it's not as easy to get that kind of balance as you'd think," McKay said, glaring up at the other man even as Ronon reached back into the gateship to toss another ARG to the Phantom.

"Thanks," John said, nodding briefly at Ronon before turning back to the matter at hand. "Right now, we've got two prisoners to rescue along with a city full of Asurans to defeat; I think we can all agree that stopping the Asurans takes priority?"

"Hostages?" Carson said, looking anxiously at John. "What makes you so sure they won't-?"

"They can't afford to send wave after wave of men at us just to stop us destroying them; it would be a waste of resources, and we're dealing with a race of machines who prefer practicality over self-sacrifice," John said firmly, before his gaze shifted to McKay. "Hostages give us something to focus on, so they'll keep them alive for the moment, but the sooner we can get that program you were talking about ready…"

"I am _working _as fast as I can; this isn't exactly a laptop, you know!" McKay said, glaring up at John as he continued tapping away at the Ancient pad in his hands.

"All right," John said, looking over at the rest of the team. "Until we can take down the Asurans, our priority has to be stealth; it shouldn't take long for the Asurans to analyse their prisoners' minds, but they don't know what we're planning yet, so we _might _have time…"

"No harm hurrying, right?" Ronon said, looking firmly at the scientist after exchanging glances with the man in the mask.

"OK, look, just let me…" McKay said, still tapping away at his gadget. "If I can… that should… yeah, OK, I think I've got his power levels about as high as I'm comfortable with; I'm gonna try to get him to-"

"_Get down_!" John yelled, raising his gun and firing it at Niam as the Asuran stood up, looking at McKay with a strong glare, only realising after he'd fired the weapon that he'd used the ARG Ronon had given him rather than his more traditional weapon.

"Oh, come _on_!" McKay said, turning to glare at the Phantom after the initial shock had passed. "I was _just _about to get somewhere-!"

"By waking him up so he could kill us all?" John said, glaring back at McKay. "I appreciate that you were trying to do something difficult, Doctor McKay, but if we're going to take back Atlantis, I think we can all agree that we're going to need a new plan."

"Can we still use the freezing program?" Doctor Beckett asked.

"Not unless we can somehow capture a Replicator and use them to upload the code without them killing us," McKay said, shooting a glare at the masked man. "I need to load the programme directly into a Replicator and spread it that way, otherwise it won't work."

"These weapons blow them apart, right?" Ronon said, holding up his own ARG. "I say we just start killing 'em."

"Normally I would share your run-and-gun enthusiasm, but these weapons are only gonna work for so long before they manage to identify the frequency they use to disrupt the bonds that hold the Replicators together," McKay said.

"In other words," John said, noting Ronon silently looking at McKay, "they build up an immunity if we shoot too many of them."

"Exactly," McKay said, nodding at the Phantom's assessment before he continued. "Look, the freezing plan would have worked because they would be unable to communicate with each other while we were blasting them, but the more we shoot, the greater the likelihood these weapons are gonna become ineffective."

"What if we had some way to hit them all at once?" John said, looking thoughtfully at the weapons in their hands. "I mean, there's a limit to how long it takes them to adapt to these weapons; if we hit enough of them in the same attack, couldn't we stop them before it's all over?"

"Yeah, that would work, if we could get them all into large groups-" McKay began, before a sudden thought occurred to him as he snapped his fingers several times, a broad grin on his face as he turned to look at Elizabeth. "How much C4 do we have?"

"Well… as much as was left in the gateship when we took it, so a decent amount; why?" Elizabeth asked.

"Well, it's desperate…" McKay said, looking around at the rest of the team.

"Well, so are we," Elizabeth said.

"We need to split into groups," McKay said.

"I was going to suggest that anyway," John said, making a mental note to do what he could to stay with Elizabeth. "Why? What are you thinking?"

* * *

AN: OK, important question; does anyone want to see the Atlantis team's efforts to rig the city shield generators and 'rescue' Jack and Woolsey, which will mostly be the same as canon, or shall we jump straight to them being captured and John being unmasked at last?


	44. Underneath the Mask

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: OK, the votes came in with a general preference for getting straight to the unmasking, so here we are; hope it proves worth it (I've had the actual unmasking written for a while, but the reactions were rather difficult to get right)

Mystery of the Phantom

As she was forced to the floor of the cell, Elizabeth tried not to show her wince as she made contact with the ground; she'd been prepared for rough treatment, but considering how rarely she was ever in physical danger in Atlantis, it still came as a bit of a shock to actually find herself being threatened inside the city.

Still, she should be grateful that everything had gone according to plan; with her and Ronon, Teyla and Carson, and McKay and John each taking responsibility for specific shield generators, they had managed to access all ten generators responsible for maintaining Atlantis's shield before they were discovered, as well as planting a fake trail for the Asurans to discover.

John had disliked being separated from her- he'd taken care not to make it obvious, but Elizabeth had been around him long enough to understand his more subtle moods, and he hadn't been happy when she'd assigned teams-, but he had accepted her reasoning for the team allocation to create a good impression on the Asurans; if the city's resident scientific genius and the legendary Phantom of Atlantis had attempted and failed to rescue the two prisoners, then the rescue team was clearly serious about trying to save them. Claiming that they intended to destroy Atlantis with C4 in the shield generators might have been a basic plan, but that was its main advantage; the C4 was so obvious as a threat that the Asurans probably wouldn't look too closely to spot what they'd really done.

On a brighter note, she'd noticed during their hurried progress through the city that the central tower had been repaired from the damage it had sustained during their arrival last night, without running into any Asurans until they were ready for them. The Asurans' attempt to activate the city's stardrive had almost been a problem, but Doctor Beckett had managed to get to the control chair and launch a few drones in time to disable the drive without damaging the city any more than necessary. Seeing Ronon taken down so easily when they were captured had been disconcerting, but Elizabeth was still confident in the plan's potential for success; they just needed to get the Asurans to take the right action now…

"Is everyone all right?" John asked, looking around at the rest of the team as they stood in their current cell, apparently awaiting the arrival of their fellow prisoners; Elizabeth was surprised to see that John was still wearing his cloak, considering all the weapons she'd seen him remove from it, but guessed that the Asurans simply hadn't thought it worth searching or removing.

"So far," Elizabeth confirmed.

"I'll be fine," Carson said.

"Why aren't we dead yet?" Ronon asked, his tone grim as he asked the question everyone else had been trying not to think about.

"They probably want to see what else we have to tell them," John said casually, before looking between the others with a slight apprehension in his eyes. "On that topic…"

"We did everything we had to do," Teyla confirmed.

"So did we… in the nick of time," Elizabeth said, recalling how the Asurans had arrived just as she was putting the last touches in place; she might have given the plan away if Ronon hadn't brought her time by engaging the Asurans in a fight.

"Me too," John said grimly. "So, all we need now is-"

He abruptly stopped himself as the cell door opened again and the Asurans walked back in, this time accompanied by General O'Neill and Mr Woolsey, who walked off into a corner of their cell.

"Did you really think you'd be able to stop us?" one of the Asurans said, looking firmly at John.

"Naturally," John said, looking at the Asuran with a slight smirk as he folded his arms. "I'm the guy who's been kicking Wraith ass for the last two decades, and you're the losers who've been sulking in your city for ten thousand years because your parents liked the other kids better."

"Excuse me?" the Asuran said, looking pointedly at John.

"You may talk about how you're so smart, but in the end you've been on your own so long that you're out of practise at doing anything other than coming in and blowing stuff up," John said, his tone becoming increasingly mocking as he looked at the Asuran; Elizabeth didn't know if she should admire John's approach or fear for his life. "Yeah, you took out the Ancients who'd settled here because you had changed your base code, but given that they weren't _prepared _for a fight, all you had to do was show up and start firing; you're still completely stupid-"

A powerful punch to John's face was followed almost immediately by the sound of metal hitting metal, but it took Elizabeth a moment to realise that the source of that sound was John's mask, lying on the ground virtually in front of her, apparently knocked off his face by the Asuran's last blow as John lay on the ground in a daze.

_He wasn't wearing his mask_…

If this had happened earlier in their… relationship… Elizabeth would have been grateful for the chance to finally learn what John looked like under that mask that had been a constant part of him ever since she'd first met him, but now she was just stricken by a sudden sense of panic at the thought; John should have been free to reveal his true appearance on his _own _terms, rather than the Asurans forcing him into that position…

"Regardless of your opinion of our abilities," the Asuran said, glaring down at the injured man, "your plan has been discovered and dealt with, _Phantom_."

As though on some silent signal, Elizabeth joined the rest of the humans in the cell in looking pointedly at Woolsey, the one most likely to have disclosed the pertinent information about the plan.

"He put his hand in my forehead," the IOA representative said indignantly. "How can you resist that?"

"Well," General O'Neill said with a casual shrug, "_I _like to close my eyes and think of England."

"Mr Woolsey informed us of everything we need to know," the Asuran said, as one of the other Asurans opened a bag and revealed one of the blocks of C4 they'd previously planted. "All of your C4 has been removed from the emitters."

"Sure about that?" John muttered from the floor, still bent over with his face pressed against the ground, apparently unwilling to get back up just yet.

"_All _generators have been accounted for, _Phantom_," the Asuran said, an edge of what could almost be called disdain in his voice despite the Asurans' normally emotionless approach. "They won't be destroyed when _Daedalus _arrives, which should be in any moment. Your plan has failed."

"_Talus_," a voice said over a radio. "_The _Daedalus _is approaching the planet_."

"As expected," the Asuran that was apparently called Talus said. "Activate the shield."

With that command, the room was briefly filled with the glowing blue energy of Atlantis's shield before the Asurans around them all collapsed into nanite piles; the plan to replace shield control crystals with the crystals from the ARGs had been a risk, but it had evidently paid off, particularly with John and McKay's fake rescue attempt to feed the Asurans additional misinformation via O'Neill and Woolsey.

"Ha!" McKay said, grinning as he looked at the piles of atomised Asurans. "It worked! I can't believe it worked!"

"What?" Woolsey said, looking at the team around him. "What just happened?"

"We turned the city shield into a giant Replicator weapon," McKay explained, looking at the two original prisoners with a grin. "They just killed _themselves_!"

"I knew it!" O'Neill said, pointing firmly at McKay.

"You knew?" Woolsey said, looking at the general indignantly.

"Well, I've seen Carter crack enough codes to know that McKay was faking the door thing," the general said with a shrug. "Add in the fact that you _were _accompanied by a guy who's meant to have been here for over two decades-"

"Jo- _Phantom_!" Elizabeth said, repeating his code name to herself as she turned to look at the masked man, still lying on the ground in a daze at the Asurans' attack…

Then John turned to look at them, responding automatically to his name being used in a friendly tone of voice, and Elizabeth was unable to stop a brief gasp of horror escaping her lips.

She'd always known that he had his reasons for not wanting her to see his face, of course- after knowing him for the better part of the last two years, and even learning his full name after Rod's visit, the idea that he had a 'secret identity' that he wanted to maintain by wearing that thing was almost too ridiculous to even think about; he'd only keep wearing the mask if there was something else prompting him to wear it- but still, it was one thing to imagine what was under there and another to actually _see_ it.

Underneath the mask, John Sheppard's face, in the most polite term that she could think of, was a mess. The right corner of his mouth was twisted upwards in an expression that evoked mental images of a snarl, made even worse by the fact that the skin around and above his left eye pressed down on the eye slightly, leaving it with a narrow glare that she'd never fully registered when he was wearing the mask; the shadow created by the eyehole made it harder to see that eye when the mask was on. His right eye, by contrast, had the skin pulled back significantly around it, giving it an impression of being perpetually widened in surprise or fear, combined with a slightly skull-like look as the eye-socket was rendered obvious to outsiders; as with his left eye, the shadow created by the mask hid the full scale of the eye from view.

The skull-like visual effect around the eye was continued by the sight of his right cheek, where the skin was so tightly pressed against the bone beneath it that she could almost swear she could see his teeth where his cheek pressed against his inner jaw. A part of the cheekbone was actually visible on the left side of his face, giving the impression that the skin had been torn off or burnt away in some accident and never had the chance to grow back. The idea that the damage had been caused in a fight of some kind was reinforced by the reddish appearance of the skin on the left side of his face, giving the skin a rough, raw appearance like it had been burnt in some past accident, the smooth lines of the Phantom's mask replaced by rough, uneven lumps of skin covering the skull.

Now that she could see his face, Elizabeth wasn't entirely sure why he'd covered it up; it wasn't exactly pleasant, but-

"WRAITHSPAWN!" Ronon and Teyla suddenly yelled, grabbing their weapons from where the Asurans had dropped them and aiming their guns at John as he lay on the ground before Elizabeth could even have the chance to speak.

The reaction from John was almost as instantaneous; before Elizabeth had even realised what he was doing, the formerly disorientated man had leapt to his feet and knocked Teyla and Ronon's weapons out of their hands with a powerful kick, subsequently grabbing them by the throats and pinning them to the wall before either of them could react.

"NEVER CALL ME THAT AGAIN!" John roared, glaring at Teyla and Ronon with a cold glare that Elizabeth had only seen him assume when he was facing Kolya during the Genii invasion.

It was only after a moment's silence that John released his grip on the two Pegasus natives, stepping back to stare at his hands in horror as Teyla and Ronon fell to the ground while the other five people in the cell looked apprehensively at him.

"Oh God…" he whispered; Elizabeth could have sworn that his eyes briefly flickered in her direction as he spoke. "No…"

Even as Elizabeth moved forward, a hand raised in an attempt to comfort him, John grabbed his mask, leapt to his feet and ran from the room, one arm pressed over his eyes while the other hand held his mask, the hero who had saved Atlantis so many times clearly too shaken to waste time putting it on.

"John, _wait_!" Elizabeth yelled, her feet sending her hurrying after John before she'd even made a conscious decision to pursue him, thoughts of keeping his name secret forgotten; she didn't know what had set John off like that, but she knew that she couldn't leave him alone…

* * *

As the head of Atlantis ran out of the cell after the man with the messed-up face, Jack made a mental note to talk with Woolsey about keeping quiet about this part of the proceedings in the aftermath (After everything that the Phantom- who appeared to be named John- and Elizabeth had just done, they both deserved some time to themselves) before he turned to look at the two Pegasus natives.

"OK," he said firmly, hoping that age would give him some authority in the absence of anyone here he officially had rank over, "while we're on our way to the control room to stop ourselves being bombed by our own guys, care to explain what just happened there?"

"He is a _Wraithspawn_-!" Teyla began, eyes wide with horror.

"Which means what exactly?" McKay asked, looking sharply at her; he was so unused to the idea of Teyla being prejudiced against something that he just wanted her to stop it so that he could focus on what really mattered.

"Wraithspawn," Ronon said grimly, even as the group began to move as quickly as possible towards the control room. "They're what happen when Wraith feed on women when they're with child; the resulting children are generally born disfigured and almost always dangerous."

Jack might not have been a science whiz, but he'd read about what happened to people who were high on the enzyme, and he knew that children whose parents were on drugs could have problems later on in life; put the two images together and he could see why people might be anxious about the results of Wraith enzyme used on pregnant women…

"And you think that the Phantom's like that?" Doctor Beckett said, looking at Ronon in surprise. "He's saved our lives more than once-"

"Wraithspawn always snap," Ronon said firmly. "We've been lucky so far at best; maybe he's not even the Phantom-"

"Well, if he's not the Phantom, I'd like to know who the hell _is _the Phantom!" McKay pointed out as they hurried around a corner. "I mean, I've been here for three years and that guy's the only guy we've seen who even might be the Phantom I've heard so much about; unless he upped stakes and left this city some time before we got here and let this guy start wearing the mask, I think we can assume he's the real deal!"

"Is anyone else… wondering… why Doctor Weir… called him John?" Woolsey asked, panting as they ran; of everyone present, he was the one in the worst shape, considering that Teyla, Ronon and Jack had all been trained soldiers (Even if Jack acknowledged he didn't get out of the office much these days) and McKay and Doctor Beckett went through a fair amount of training in Atlantis, and was therefore lagging behind the others.

"Actually… well, I noticed it, but maybe it's-" McKay began, taken aback at the simplicity of the question.

"It's because that's his name…" Doctor Beckett said, with a tone of realisation in his voice despite the fatigue as he continued to run. "He's John Sheppard!"

"He's who?" Jack asked, looking at the doctor in confusion.

"Well… you were told about our encounter with an alternate universe a month before we found the _Tria_, right?" Beckett asked, looking curiously at the colonel as they began to hurry up the stairs towards the control room.

"You mean when the other McKay came through because what we were doing was screwing things up on his end?" Jack said, briefly indicating the Canadian in question for confirmation. "Yeah, I got that."

"Well, while he was here, Rod mentioned a Colonel John Sheppard who possessed the strongest Ancient gene in the expedition in his world," Doctor Beckett explained, a slight smile on his face as he ran. "I tried to look for information about him when I got back to Earth- I thought that it might be useful to find him and bring him in-, but discounting any John Sheppards who were too old or too young to have achieved that rank by now, and a few other possibilities, the best candidate I found was a John Sheppard who'd vanished from Earth about twenty years ago on a family holiday."

"And you think this is _him_?" McKay said, looking at the city's chief physician in surprise. "You think this… Phantom guy is _that _John Sheppard?"

"Then… he is from Earth?" Teyla said in surprise. "But… his face-"

"Yeah, yeah, that's fascinating and all, and it's probably a good guess, but can we just focus on the fact that we're going to get hit with a large load of nuclear bombs if we don't get to that control room?" Jack asked, trying to pick up the pace as they ran.

He had to admit that he found Beckett's theory interesting, even if there were still several questions that needed answering before he'd consider it a definite possibility, but right now Jack had to deal with the more immediate concern of telling Colonel Caldwell that they were back in control of the city; they'd worry about the guy in the mask with the messed-up face later.

* * *

Even as she ran, Elizabeth wasn't sure what she intended to accomplish; if John was serious about getting away, she knew that he knew enough about Atlantis to make it virtually impossible for her to find him if he didn't want to be found.

All she could do at this point was keep on hurrying after him and hope that John's obvious shock would be enough to stop him doing anything too complicated to get away from her. As she ran around a corner, she saw John's cloak hurrying towards a transporter, but managed to put on an extra burst of speed and dive through the transporter doors before they could close, leaving John staring at her in shock, his disfigured face still obvious as his mask was clutched in his hand.

"What-?" he began.

"John," Elizabeth interrupted, staring firmly at him- he appeared to be calmer now, but his earlier anger wasn't something she'd forget; she had to keep him focused on the situation at hand-, "I know that Teyla and Ronon's reaction to you was extreme, but-"

"Actually, it wasn't," John said, staring solemnly at her. "Compared to some of the reactions I've received, that was relatively tame."

"_Tame_?" Elizabeth repeated incredulously; with John acting so much calmer now, it was easier to forget what he'd done to Teyla and Ronon just moments ago and focus on him as the man she'd come to know over the years, even with his new, twisted face. "John, they tried to _attack _you-!"

"I spent months dealing with that kind of reaction from entire villages before I got the mask together back when I started hunting Wraith," John said with a grim smile. "After a while, I was so used to the idea that people would start attacking me when they saw my face that it was easier to wear that mask all the time than get screamed at again; two people about to shoot me doesn't count as extreme…"

Elizabeth couldn't believe it; John had experienced worse than what she'd just seen from people when he'd done nothing but try and help them… and he considered that _all right_?

"But… why?" she asked, looking at him in confusion, suddenly stuck for what she should do next when faced with an unmasked John who was actually answering personal questions about his pre-Phantom life; everything she'd known seemed to have been rendered useless since he took that mask off. "I mean, I admire what you did, but if you were getting that reaction… why do it in the first place? Why not just… well…?"

"Leave them to their fate after the first few planets I visited started screaming at me?" John finished for her, his smile still grim as he looked at her. "Someone very important made me promise that I'd never abandon the innocent to their fate like that, and I had to keep that promise."

"What promise?" Elizabeth asked; if the idea of John talking about his past was a surprise, the idea that someone else had inspired him to become the Phantom was even more of a shock. "Who could mean that much to you?"

For a moment, John stared thoughtfully at her, his expression contemplative, before he sighed and nodded.

"After everything else we've been through," he said, nodding grimly at her, "it's time you learned the truth."

With that statement, he turned to the transporter's control panel and pressed a button on a section of the city that Elizabeth had never known possessed a transporter, the doors opening to reveal a darkened corridor. Before Elizabeth could ask what he was doing, John walked out of the transporter and headed towards a door further down the corridor, opening it as Elizabeth caught up with him. Inside the room, she was surprised to find nothing more than a glass chamber in one corner with a woman inside it. The woman was wearing a simple long white dress and had hair so white it was almost silver reaching down past her shoulders, her face surprisingly smooth despite the lines of age, her eyes closed in a peaceful manner that left it unclear if she was sleeping or… something else.

"Who is she?" Elizabeth asked, staring at the old woman in surprise, not realising that she'd spoken in a whisper until she'd done so; something about this whole room gave the impression that she was in a shrine…

"She was my guardian angel," John said, a smile on his face the only sign that the term he'd just used was a slight joke even to himself as he reached out to stroke the glass chamber, staring wistfully at the woman within it. "She taught me all that she could about the history of Atlantis, the technology it possessed, where I could find the first of the ZPMs I'd need, how to use the database, how to read it…"

His smile became more solemn as he reached out to place his hand on the glass, looking at the woman lying within the stasis tube with a tenderness that clearly showed how much this woman meant to him. "She gave my life meaning and believed in me when nobody else ever did, and I couldn't save her…"

"Who was she?" Elizabeth asked again, looking curiously at the figure in the tube.

"Oh, you know her," John said, looking back at her with a smile. "Her name was Doctor Elizabeth Weir."

* * *

AN 2: And there we have it; John's mask has been removed, his name disclosed, and he has revealed his connection with the time-displaced Elizabeth to the current Elizabeth.

Coming up next, I answer the question of how John got here and what happened to his face in the first place, as well as looking at his first meeting with the time-displaced Elizabeth Weir, as he began the journey that would turn him into the Phantom…


End file.
